Starting phenix.real_space_refine on Wed Sep 25 19:52:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o3l_3741/09_2024/5o3l_3741.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o3l_3741/09_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_3741/09_2024/5o3l_3741.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o3l_3741/09_2024/5o3l_3741.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o3l_3741/09_2024/5o3l_3741.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o3l_3741/09_2024/5o3l_3741.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 5.49, per 1000 atoms: 0.48 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 - 3.00 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: 2.66 Conformation dependent library (CDL) restraints added in 787.0 milliseconds 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: 1.51 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 3.23 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: 0.00 - 1.27: 16358 1.27 - 2.54: 2770 2.54 - 3.82: 1581 3.82 - 5.09: 151 5.09 - 6.36: 40 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 2.450 nonbonded pdb=" O SER H 316 " pdb=" HG SER J 316 " model vdw 1.419 2.450 nonbonded pdb=" O SER B 316 " pdb=" HG SER D 316 " model vdw 1.419 2.450 nonbonded pdb=" O SER F 316 " pdb=" HG SER H 316 " model vdw 1.420 2.450 nonbonded pdb=" HG SER F 320 " pdb=" OD1 ASN F 368 " model vdw 1.420 2.450 ... (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 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 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: 0.230 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 22.270 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.240 ------------------------------------------------------------------------------- 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 : 0.884 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: 0.5591 time to fit residues: 202.5576 Evaluate side-chains 221 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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: 0.5980 chunk 53 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 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 368 ASN B 368 ASN C 359 ASN C 368 ASN D 359 ASN D 368 ASN E 336 GLN E 359 ASN E 368 ASN F 368 ASN G 368 ASN H 368 ASN H 374 HIS I 368 ASN J 368 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5660 Z= 0.175 Angle : 0.789 7.123 7580 Z= 0.390 Chirality : 0.052 0.141 860 Planarity : 0.007 0.049 960 Dihedral : 6.977 19.271 740 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.44 % Favored : 80.56 % Rotamer: Outliers : 2.19 % Allowed : 16.72 % Favored : 81.09 % 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: -6.57 (0.15), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.00 (0.11), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 362 PHE 0.009 0.001 PHE F 378 TYR 0.014 0.002 TYR C 310 ARG 0.006 0.001 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 263 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 249 time to evaluate : 0.853 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 outliers start: 14 outliers final: 11 residues processed: 254 average time/residue: 0.5037 time to fit residues: 154.8320 Evaluate side-chains 227 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 216 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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: 3.9990 chunk 19 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 68 optimal weight: 0.1980 chunk 56 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 62 optimal weight: 0.3980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.6111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5660 Z= 0.165 Angle : 0.743 5.972 7580 Z= 0.368 Chirality : 0.051 0.178 860 Planarity : 0.007 0.050 960 Dihedral : 6.573 17.947 740 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.18 % Favored : 82.82 % Rotamer: Outliers : 2.50 % Allowed : 17.66 % 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: -6.51 (0.15), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.95 (0.11), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 362 PHE 0.005 0.001 PHE H 378 TYR 0.010 0.002 TYR A 310 ARG 0.004 0.001 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 252 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 236 time to evaluate : 1.028 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: 0.6505 (p0) cc_final: 0.6271 (p0) REVERT: D 358 ASP cc_start: 0.6433 (p0) cc_final: 0.6212 (p0) REVERT: E 358 ASP cc_start: 0.5802 (p0) cc_final: 0.5463 (p0) outliers start: 16 outliers final: 13 residues processed: 245 average time/residue: 0.4955 time to fit residues: 148.7061 Evaluate side-chains 231 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 218 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 359 ASN Chi-restraints excluded: chain D residue 351 GLN 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 G residue 325 LEU Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain H 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: 0.9980 chunk 33 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 56 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.6606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5660 Z= 0.140 Angle : 0.680 6.462 7580 Z= 0.337 Chirality : 0.049 0.130 860 Planarity : 0.006 0.052 960 Dihedral : 6.037 17.835 740 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.03 % Favored : 81.97 % Rotamer: Outliers : 3.12 % Allowed : 17.97 % Favored : 78.91 % 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: -6.33 (0.15), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.82 (0.12), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 362 PHE 0.004 0.001 PHE C 378 TYR 0.014 0.002 TYR A 310 ARG 0.005 0.001 ARG I 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 260 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 240 time to evaluate : 0.932 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: 0.6702 (mtp180) cc_final: 0.6446 (mtp180) REVERT: B 358 ASP cc_start: 0.6662 (p0) cc_final: 0.6358 (p0) REVERT: D 358 ASP cc_start: 0.6526 (p0) cc_final: 0.6304 (p0) REVERT: E 358 ASP cc_start: 0.5868 (p0) cc_final: 0.5576 (p0) outliers start: 20 outliers final: 17 residues processed: 250 average time/residue: 0.4570 time to fit residues: 140.7135 Evaluate side-chains 241 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 224 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 351 GLN Chi-restraints excluded: chain E residue 307 GLN 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 G residue 325 LEU Chi-restraints excluded: chain G residue 351 GLN Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain H residue 325 LEU Chi-restraints excluded: chain I residue 306 VAL 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: 1.9990 chunk 57 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.6981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5660 Z= 0.203 Angle : 0.696 4.852 7580 Z= 0.342 Chirality : 0.049 0.181 860 Planarity : 0.006 0.048 960 Dihedral : 5.933 17.605 740 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.90 % Favored : 83.10 % Rotamer: Outliers : 3.59 % Allowed : 19.38 % Favored : 77.03 % 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: -6.20 (0.16), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.72 (0.12), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 362 PHE 0.005 0.001 PHE B 346 TYR 0.011 0.002 TYR F 310 ARG 0.006 0.001 ARG I 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 264 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 241 time to evaluate : 0.941 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: 0.6732 (p0) cc_final: 0.6441 (p0) REVERT: D 358 ASP cc_start: 0.6688 (p0) cc_final: 0.6418 (p0) REVERT: E 342 GLU cc_start: 0.5110 (mm-30) cc_final: 0.4858 (mm-30) outliers start: 23 outliers final: 19 residues processed: 251 average time/residue: 0.4604 time to fit residues: 141.9847 Evaluate side-chains 247 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 228 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU 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 E residue 307 GLN 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 338 GLU 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 307 GLN Chi-restraints excluded: chain H residue 325 LEU Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain I residue 314 ASP Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain J residue 371 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 56 optimal weight: 0.0870 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 359 ASN ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.7296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5660 Z= 0.135 Angle : 0.673 6.594 7580 Z= 0.328 Chirality : 0.049 0.187 860 Planarity : 0.006 0.055 960 Dihedral : 5.666 16.721 740 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.34 % Favored : 83.66 % Rotamer: Outliers : 3.12 % Allowed : 20.78 % Favored : 76.09 % 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: -6.06 (0.16), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.61 (0.12), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 330 PHE 0.004 0.001 PHE C 378 TYR 0.012 0.002 TYR F 310 ARG 0.007 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 260 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 240 time to evaluate : 0.883 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: 0.6657 (p0) cc_final: 0.6340 (p0) REVERT: D 358 ASP cc_start: 0.6645 (p0) cc_final: 0.6398 (p0) outliers start: 20 outliers final: 18 residues processed: 250 average time/residue: 0.4558 time to fit residues: 142.9782 Evaluate side-chains 252 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 234 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 307 GLN 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 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 307 GLN Chi-restraints excluded: chain H residue 325 LEU Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain J residue 307 GLN 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: 3.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.7407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5660 Z= 0.179 Angle : 0.679 4.968 7580 Z= 0.332 Chirality : 0.048 0.157 860 Planarity : 0.006 0.053 960 Dihedral : 5.652 17.248 740 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.93 % Favored : 85.07 % Rotamer: Outliers : 3.44 % Allowed : 20.47 % Favored : 76.09 % 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: -5.97 (0.16), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.54 (0.12), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 362 PHE 0.005 0.001 PHE B 346 TYR 0.013 0.002 TYR A 310 ARG 0.006 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 257 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 235 time to evaluate : 1.070 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: 0.6682 (p0) cc_final: 0.6409 (p0) REVERT: D 358 ASP cc_start: 0.6769 (p0) cc_final: 0.6507 (p0) outliers start: 22 outliers final: 21 residues processed: 245 average time/residue: 0.4221 time to fit residues: 129.2886 Evaluate side-chains 250 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 229 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain E residue 307 GLN 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 F residue 307 GLN 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 307 GLN Chi-restraints excluded: chain H residue 325 LEU Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain J residue 307 GLN Chi-restraints excluded: chain J residue 371 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.0470 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 6 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 359 ASN ** F 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.7637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5660 Z= 0.142 Angle : 0.666 4.896 7580 Z= 0.323 Chirality : 0.048 0.140 860 Planarity : 0.006 0.062 960 Dihedral : 5.520 16.711 740 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.20 % Favored : 83.80 % Rotamer: Outliers : 3.59 % Allowed : 20.94 % Favored : 75.47 % 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: -5.84 (0.17), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.44 (0.13), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 330 PHE 0.004 0.001 PHE B 346 TYR 0.017 0.002 TYR A 310 ARG 0.005 0.001 ARG I 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 267 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 244 time to evaluate : 1.029 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: B 358 ASP cc_start: 0.6674 (p0) cc_final: 0.6363 (p0) REVERT: D 358 ASP cc_start: 0.6755 (p0) cc_final: 0.6476 (p0) REVERT: E 358 ASP cc_start: 0.6593 (p0) cc_final: 0.6369 (p0) outliers start: 23 outliers final: 23 residues processed: 255 average time/residue: 0.4274 time to fit residues: 137.5742 Evaluate side-chains 257 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 234 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 307 GLN Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain E residue 307 GLN 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 338 GLU 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 307 GLN Chi-restraints excluded: chain H residue 325 LEU Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain J residue 307 GLN Chi-restraints excluded: chain J residue 371 ILE 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: 2.9990 chunk 19 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 66 optimal weight: 0.4980 chunk 40 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.7799 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= 0.136 Angle : 0.682 5.279 7580 Z= 0.329 Chirality : 0.049 0.142 860 Planarity : 0.006 0.052 960 Dihedral : 5.482 17.629 740 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.66 % Favored : 86.34 % Rotamer: Outliers : 3.44 % Allowed : 22.66 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.75 (0.17), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.38 (0.13), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 330 PHE 0.004 0.001 PHE B 346 TYR 0.015 0.002 TYR A 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 258 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 236 time to evaluate : 0.881 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: 0.6685 (p0) cc_final: 0.6367 (p0) REVERT: D 358 ASP cc_start: 0.6738 (p0) cc_final: 0.6459 (p0) REVERT: J 311 LYS cc_start: 0.5038 (tppt) cc_final: 0.4830 (tppt) outliers start: 22 outliers final: 18 residues processed: 246 average time/residue: 0.4310 time to fit residues: 132.1912 Evaluate side-chains 249 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 231 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain E residue 307 GLN 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 F residue 307 GLN 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 325 LEU Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain J residue 307 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 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: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 359 ASN ** F 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.7948 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= 0.154 Angle : 0.680 5.338 7580 Z= 0.328 Chirality : 0.048 0.139 860 Planarity : 0.006 0.060 960 Dihedral : 5.434 16.890 740 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.48 % Favored : 83.52 % Rotamer: Outliers : 3.28 % Allowed : 24.06 % Favored : 72.66 % 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: -5.63 (0.18), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.29 (0.13), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 330 PHE 0.006 0.001 PHE G 346 TYR 0.014 0.002 TYR A 310 ARG 0.004 0.001 ARG J 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 258 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 237 time to evaluate : 1.038 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: 0.6697 (p0) cc_final: 0.6373 (p0) REVERT: D 358 ASP cc_start: 0.6798 (p0) cc_final: 0.6533 (p0) REVERT: J 311 LYS cc_start: 0.5158 (tppt) cc_final: 0.4902 (tppt) outliers start: 21 outliers final: 19 residues processed: 247 average time/residue: 0.4207 time to fit residues: 129.9585 Evaluate side-chains 248 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 229 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU 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 351 GLN Chi-restraints excluded: chain E residue 307 GLN 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 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 307 GLN Chi-restraints excluded: chain H residue 325 LEU Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain J residue 307 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 368 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 = 0.4755 r_free = 0.4755 target = 0.162378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.142880 restraints weight = 26614.492| |-----------------------------------------------------------------------------| r_work (start): 0.4535 rms_B_bonded: 3.24 r_work: 0.4526 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.4413 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.4413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.7989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.241 5660 Z= 0.298 Angle : 1.099 59.190 7580 Z= 0.638 Chirality : 0.048 0.200 860 Planarity : 0.006 0.059 960 Dihedral : 5.525 28.012 740 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.92 % Favored : 84.08 % Rotamer: Outliers : 2.97 % Allowed : 24.06 % Favored : 72.97 % 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: -5.62 (0.18), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.27 (0.13), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 330 PHE 0.005 0.001 PHE G 346 TYR 0.013 0.002 TYR A 310 ARG 0.002 0.001 ARG H 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4576.57 seconds wall clock time: 81 minutes 4.92 seconds (4864.92 seconds total)