Starting phenix.real_space_refine on Tue Jun 10 00:05:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5o3l_3741/06_2025/5o3l_3741.cif Found real_map, /net/cci-nas-00/data/ceres_data/5o3l_3741/06_2025/5o3l_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/cci-nas-00/data/ceres_data/5o3l_3741/06_2025/5o3l_3741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5o3l_3741/06_2025/5o3l_3741.map" model { file = "/net/cci-nas-00/data/ceres_data/5o3l_3741/06_2025/5o3l_3741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5o3l_3741/06_2025/5o3l_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-5710/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: 5.76, per 1000 atoms: 0.51 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: 2.64 Conformation dependent library (CDL) restraints added in 681.5 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: 1.33 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: 3.27 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain '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: 0.880 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: 0.210 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.120 Process input model: 22.300 Find NCS groups from input model: 0.170 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: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.100 ------------------------------------------------------------------------------- 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 Details of bonding type rmsd covalent geometry : bond 0.01229 ( 5660) covalent geometry : angle 1.03443 ( 7580) *********************** 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 to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 0.923 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: 0.5553 time to fit residues: 201.3032 Evaluate side-chains 221 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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: 3.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.172442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.153712 restraints weight = 27215.716| |-----------------------------------------------------------------------------| r_work (start): 0.4598 rms_B_bonded: 3.18 r_work: 0.4646 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.4544 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.4544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 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 7.124 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 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 5660) covalent geometry : angle 0.78920 ( 7580) *********************** 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 to be fit. rotamer outliers: 14 poor density : 249 time to evaluate : 0.855 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: A 372 GLU cc_start: 0.8205 (mp0) cc_final: 0.7770 (mp0) REVERT: B 347 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8349 (mtmm) REVERT: C 363 VAL cc_start: 0.9293 (t) cc_final: 0.9033 (p) REVERT: C 370 LYS cc_start: 0.7843 (tttm) cc_final: 0.7298 (tttm) REVERT: D 349 ARG cc_start: 0.8054 (mtm-85) cc_final: 0.7802 (mtp180) REVERT: D 363 VAL cc_start: 0.9341 (t) cc_final: 0.9112 (p) REVERT: E 342 GLU cc_start: 0.7489 (mp0) cc_final: 0.6955 (mp0) REVERT: E 349 ARG cc_start: 0.8191 (mtm-85) cc_final: 0.7947 (mtp180) REVERT: E 372 GLU cc_start: 0.7517 (mp0) cc_final: 0.7088 (mp0) REVERT: I 307 GLN cc_start: 0.7913 (tt0) cc_final: 0.6991 (mp10) REVERT: I 308 ILE cc_start: 0.8152 (tt) cc_final: 0.7946 (tt) REVERT: J 321 LYS cc_start: 0.9048 (tttm) cc_final: 0.8836 (tttm) outliers start: 14 outliers final: 11 residues processed: 254 average time/residue: 0.5100 time to fit residues: 158.5980 Evaluate side-chains 229 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 217 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 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 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 12 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 61 optimal weight: 0.0970 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.170845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.151604 restraints weight = 27443.349| |-----------------------------------------------------------------------------| r_work (start): 0.4600 rms_B_bonded: 3.40 r_work: 0.4644 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.4538 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.4538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.5945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5660 Z= 0.164 Angle : 0.728 5.447 7580 Z= 0.364 Chirality : 0.051 0.154 860 Planarity : 0.007 0.049 960 Dihedral : 6.529 18.331 740 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.61 % Favored : 82.39 % Rotamer: Outliers : 2.50 % Allowed : 17.97 % Favored : 79.53 % 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 : -4.96 (0.11), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 362 PHE 0.005 0.001 PHE H 378 TYR 0.011 0.002 TYR A 310 ARG 0.004 0.000 ARG I 349 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 5660) covalent geometry : angle 0.72812 ( 7580) *********************** 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 253 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 237 time to evaluate : 0.856 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 372 GLU cc_start: 0.8205 (mp0) cc_final: 0.7672 (mp0) REVERT: B 347 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8251 (mtmm) REVERT: B 358 ASP cc_start: 0.8578 (p0) cc_final: 0.8337 (p0) REVERT: C 340 LYS cc_start: 0.8745 (ttmt) cc_final: 0.8536 (tptp) REVERT: C 363 VAL cc_start: 0.9300 (t) cc_final: 0.9069 (p) REVERT: D 358 ASP cc_start: 0.8729 (p0) cc_final: 0.8423 (p0) REVERT: D 372 GLU cc_start: 0.8249 (mt-10) cc_final: 0.8042 (mp0) REVERT: E 349 ARG cc_start: 0.8188 (mtm-85) cc_final: 0.7884 (mtp85) REVERT: E 358 ASP cc_start: 0.8075 (p0) cc_final: 0.7770 (p0) REVERT: I 307 GLN cc_start: 0.7954 (tt0) cc_final: 0.7025 (mp10) REVERT: I 345 ASP cc_start: 0.8039 (m-30) cc_final: 0.7721 (t0) outliers start: 16 outliers final: 13 residues processed: 246 average time/residue: 0.4886 time to fit residues: 147.1853 Evaluate side-chains 234 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 220 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 347 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 17 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 0.0770 overall best weight: 0.9942 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.167357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.148207 restraints weight = 27497.331| |-----------------------------------------------------------------------------| r_work (start): 0.4545 rms_B_bonded: 3.30 r_work: 0.4596 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.4487 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.4487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.6433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5660 Z= 0.184 Angle : 0.699 6.711 7580 Z= 0.349 Chirality : 0.050 0.168 860 Planarity : 0.006 0.050 960 Dihedral : 6.161 18.253 740 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.03 % Favored : 81.97 % Rotamer: Outliers : 3.28 % Allowed : 17.66 % 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: -6.41 (0.15), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.88 (0.11), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 362 PHE 0.004 0.001 PHE C 378 TYR 0.012 0.002 TYR A 310 ARG 0.006 0.001 ARG I 349 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 5660) covalent geometry : angle 0.69916 ( 7580) *********************** 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 258 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 237 time to evaluate : 0.871 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: 0.8647 (mtp180) cc_final: 0.8291 (mtp180) REVERT: B 311 LYS cc_start: 0.7540 (pptt) cc_final: 0.7134 (pptt) REVERT: B 347 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8193 (mtmm) REVERT: B 358 ASP cc_start: 0.8807 (p0) cc_final: 0.8431 (p0) REVERT: B 372 GLU cc_start: 0.8459 (mp0) cc_final: 0.8110 (mp0) REVERT: C 363 VAL cc_start: 0.9333 (t) cc_final: 0.8989 (p) REVERT: D 358 ASP cc_start: 0.8810 (p0) cc_final: 0.8565 (p0) REVERT: E 363 VAL cc_start: 0.9304 (t) cc_final: 0.9038 (p) REVERT: H 342 GLU cc_start: 0.8033 (mp0) cc_final: 0.7463 (mp0) REVERT: I 307 GLN cc_start: 0.8066 (tt0) cc_final: 0.7152 (mp10) REVERT: I 345 ASP cc_start: 0.8224 (m-30) cc_final: 0.7831 (t0) REVERT: J 345 ASP cc_start: 0.8360 (m-30) cc_final: 0.7794 (t0) outliers start: 21 outliers final: 15 residues processed: 249 average time/residue: 0.4700 time to fit residues: 146.0259 Evaluate side-chains 233 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 217 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 347 LYS 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 358 ASP 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 33 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 54 optimal weight: 0.1980 chunk 48 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.165530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.146998 restraints weight = 27156.526| |-----------------------------------------------------------------------------| r_work (start): 0.4548 rms_B_bonded: 3.20 r_work: 0.4598 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.4488 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.4488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.6881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5660 Z= 0.170 Angle : 0.692 4.780 7580 Z= 0.340 Chirality : 0.050 0.176 860 Planarity : 0.006 0.049 960 Dihedral : 5.876 18.069 740 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.62 % Favored : 83.38 % Rotamer: Outliers : 3.59 % Allowed : 19.69 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.22 (0.16), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.74 (0.12), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 362 PHE 0.005 0.001 PHE B 346 TYR 0.013 0.002 TYR F 310 ARG 0.007 0.001 ARG B 349 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 5660) covalent geometry : angle 0.69247 ( 7580) *********************** 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 259 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 236 time to evaluate : 1.000 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: 0.8637 (mtp180) cc_final: 0.8316 (mtp180) REVERT: A 358 ASP cc_start: 0.8800 (p0) cc_final: 0.8596 (p0) REVERT: B 347 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8138 (mtmm) REVERT: B 358 ASP cc_start: 0.8739 (p0) cc_final: 0.8376 (p0) REVERT: B 372 GLU cc_start: 0.8361 (mp0) cc_final: 0.7905 (mp0) REVERT: C 363 VAL cc_start: 0.9302 (t) cc_final: 0.8971 (p) REVERT: D 325 LEU cc_start: 0.7614 (mt) cc_final: 0.6939 (mt) REVERT: D 358 ASP cc_start: 0.8902 (p0) cc_final: 0.8654 (p0) REVERT: E 363 VAL cc_start: 0.9262 (t) cc_final: 0.9060 (p) REVERT: F 345 ASP cc_start: 0.8239 (m-30) cc_final: 0.7664 (t0) REVERT: G 349 ARG cc_start: 0.8224 (mtp180) cc_final: 0.7746 (mtm-85) REVERT: H 342 GLU cc_start: 0.8181 (mp0) cc_final: 0.7618 (mp0) REVERT: I 307 GLN cc_start: 0.8105 (tt0) cc_final: 0.7195 (mp10) REVERT: I 345 ASP cc_start: 0.8314 (m-30) cc_final: 0.8025 (t0) REVERT: J 345 ASP cc_start: 0.8456 (m-30) cc_final: 0.7940 (t0) outliers start: 23 outliers final: 19 residues processed: 248 average time/residue: 0.4473 time to fit residues: 137.6972 Evaluate side-chains 244 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 224 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 B residue 347 LYS 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 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 359 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 22 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 = 0.4779 r_free = 0.4779 target = 0.165320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.146325 restraints weight = 27377.591| |-----------------------------------------------------------------------------| r_work (start): 0.4570 rms_B_bonded: 3.36 r_work: 0.4616 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.4501 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.4501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.7180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5660 Z= 0.146 Angle : 0.669 7.150 7580 Z= 0.326 Chirality : 0.048 0.131 860 Planarity : 0.006 0.051 960 Dihedral : 5.670 17.739 740 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.89 % Favored : 82.11 % Rotamer: Outliers : 3.28 % Allowed : 19.69 % 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: -6.07 (0.16), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.62 (0.12), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 330 PHE 0.005 0.001 PHE I 378 TYR 0.012 0.002 TYR F 310 ARG 0.005 0.001 ARG I 349 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 5660) covalent geometry : angle 0.66928 ( 7580) *********************** 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 261 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 240 time to evaluate : 1.136 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 321 LYS cc_start: 0.6281 (pptt) cc_final: 0.5464 (pttm) REVERT: A 349 ARG cc_start: 0.8626 (mtp180) cc_final: 0.8331 (mtp180) REVERT: B 311 LYS cc_start: 0.7339 (pptt) cc_final: 0.6786 (pptt) REVERT: B 347 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8109 (mtmm) REVERT: B 353 LYS cc_start: 0.9121 (mtmt) cc_final: 0.8742 (mtpp) REVERT: B 358 ASP cc_start: 0.8785 (p0) cc_final: 0.8413 (p0) REVERT: C 363 VAL cc_start: 0.9254 (t) cc_final: 0.8989 (p) REVERT: D 345 ASP cc_start: 0.7811 (t0) cc_final: 0.7534 (t0) REVERT: D 358 ASP cc_start: 0.8912 (p0) cc_final: 0.8618 (p0) REVERT: F 345 ASP cc_start: 0.8138 (m-30) cc_final: 0.7789 (t0) REVERT: G 345 ASP cc_start: 0.8446 (m-30) cc_final: 0.7957 (t0) REVERT: H 342 GLU cc_start: 0.8152 (mp0) cc_final: 0.7631 (mp0) REVERT: H 363 VAL cc_start: 0.9276 (t) cc_final: 0.8919 (p) REVERT: I 307 GLN cc_start: 0.8157 (tt0) cc_final: 0.7234 (mp10) REVERT: I 345 ASP cc_start: 0.8444 (m-30) cc_final: 0.8138 (t0) REVERT: J 345 ASP cc_start: 0.8451 (m-30) cc_final: 0.8011 (t0) REVERT: J 353 LYS cc_start: 0.9313 (mtmt) cc_final: 0.9019 (mtmt) outliers start: 21 outliers final: 19 residues processed: 251 average time/residue: 0.4966 time to fit residues: 154.8735 Evaluate side-chains 249 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 229 time to evaluate : 1.445 ------------------------------------------------------------------------------- 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 347 LYS 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 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 359 ASN Chi-restraints excluded: chain J residue 371 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 55 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 336 GLN J 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.151417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.131935 restraints weight = 28407.988| |-----------------------------------------------------------------------------| r_work (start): 0.4394 rms_B_bonded: 3.15 r_work: 0.4376 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.4264 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.7630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 5660 Z= 0.345 Angle : 0.801 5.973 7580 Z= 0.396 Chirality : 0.051 0.159 860 Planarity : 0.006 0.049 960 Dihedral : 6.241 18.625 740 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.56 % Favored : 79.44 % Rotamer: Outliers : 4.06 % Allowed : 20.94 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.99 (0.16), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.56 (0.12), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 329 PHE 0.008 0.001 PHE B 346 TYR 0.016 0.002 TYR A 310 ARG 0.006 0.001 ARG I 349 Details of bonding type rmsd covalent geometry : bond 0.00753 ( 5660) covalent geometry : angle 0.80065 ( 7580) *********************** 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 259 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 233 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.8721 (mtp180) cc_final: 0.8427 (mtp180) REVERT: A 372 GLU cc_start: 0.8164 (mp0) cc_final: 0.7824 (mp0) REVERT: B 353 LYS cc_start: 0.9196 (mtmt) cc_final: 0.8835 (mtpp) REVERT: B 358 ASP cc_start: 0.8890 (p0) cc_final: 0.8525 (p0) REVERT: B 376 LEU cc_start: 0.8407 (tp) cc_final: 0.8144 (tt) REVERT: D 319 THR cc_start: 0.8649 (m) cc_final: 0.8429 (m) REVERT: D 325 LEU cc_start: 0.8029 (mt) cc_final: 0.7453 (mt) REVERT: D 345 ASP cc_start: 0.8122 (t0) cc_final: 0.7887 (t0) REVERT: D 358 ASP cc_start: 0.9001 (p0) cc_final: 0.8692 (p0) REVERT: E 358 ASP cc_start: 0.8769 (p0) cc_final: 0.8555 (p0) REVERT: F 342 GLU cc_start: 0.8352 (mp0) cc_final: 0.8006 (mp0) REVERT: F 345 ASP cc_start: 0.8376 (m-30) cc_final: 0.8140 (t0) REVERT: G 345 ASP cc_start: 0.8618 (m-30) cc_final: 0.8029 (t0) REVERT: H 342 GLU cc_start: 0.8200 (mp0) cc_final: 0.7729 (mp0) REVERT: I 307 GLN cc_start: 0.8282 (tt0) cc_final: 0.7290 (mp10) REVERT: I 336 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7699 (tt0) REVERT: I 345 ASP cc_start: 0.8683 (m-30) cc_final: 0.8295 (t0) REVERT: I 373 THR cc_start: 0.8803 (m) cc_final: 0.8306 (p) REVERT: J 311 LYS cc_start: 0.5723 (tppt) cc_final: 0.5429 (tppt) REVERT: J 345 ASP cc_start: 0.8558 (m-30) cc_final: 0.8285 (t0) REVERT: J 353 LYS cc_start: 0.9265 (mtmt) cc_final: 0.8960 (mtmt) REVERT: J 372 GLU cc_start: 0.7866 (mp0) cc_final: 0.7656 (mp0) outliers start: 26 outliers final: 19 residues processed: 244 average time/residue: 0.4435 time to fit residues: 135.6493 Evaluate side-chains 243 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 223 time to evaluate : 1.227 ------------------------------------------------------------------------------- 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 307 GLN Chi-restraints excluded: chain E residue 307 GLN 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 314 ASP Chi-restraints excluded: chain I residue 336 GLN Chi-restraints excluded: chain I residue 359 ASN Chi-restraints excluded: chain J residue 307 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 14 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** ** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 = 0.4695 r_free = 0.4695 target = 0.156615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.137153 restraints weight = 27346.381| |-----------------------------------------------------------------------------| r_work (start): 0.4460 rms_B_bonded: 3.26 r_work: 0.4451 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.4339 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.7843 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= 0.154 Angle : 0.710 5.369 7580 Z= 0.345 Chirality : 0.050 0.169 860 Planarity : 0.006 0.060 960 Dihedral : 5.860 18.494 740 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.03 % Favored : 81.97 % Rotamer: Outliers : 3.28 % Allowed : 22.19 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.87 (0.16), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.47 (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 I 346 TYR 0.019 0.002 TYR A 310 ARG 0.002 0.001 ARG J 349 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 5660) covalent geometry : angle 0.71012 ( 7580) *********************** 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 260 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 239 time to evaluate : 0.889 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: A 349 ARG cc_start: 0.8703 (mtp180) cc_final: 0.8431 (mtp180) REVERT: A 372 GLU cc_start: 0.8210 (mp0) cc_final: 0.7831 (mp0) REVERT: B 353 LYS cc_start: 0.9184 (mtmt) cc_final: 0.8835 (mtpp) REVERT: B 358 ASP cc_start: 0.8879 (p0) cc_final: 0.8570 (p0) REVERT: B 376 LEU cc_start: 0.8375 (tp) cc_final: 0.8142 (tt) REVERT: D 319 THR cc_start: 0.8622 (m) cc_final: 0.8408 (m) REVERT: D 325 LEU cc_start: 0.7715 (mt) cc_final: 0.6962 (mt) REVERT: D 345 ASP cc_start: 0.8074 (t0) cc_final: 0.7827 (t0) REVERT: D 358 ASP cc_start: 0.9018 (p0) cc_final: 0.8670 (p0) REVERT: E 358 ASP cc_start: 0.8777 (p0) cc_final: 0.8566 (p0) REVERT: F 345 ASP cc_start: 0.8404 (m-30) cc_final: 0.8127 (t0) REVERT: G 345 ASP cc_start: 0.8453 (m-30) cc_final: 0.7920 (t0) REVERT: H 342 GLU cc_start: 0.8242 (mp0) cc_final: 0.7793 (mp0) REVERT: I 307 GLN cc_start: 0.8262 (tt0) cc_final: 0.7267 (mp10) REVERT: I 345 ASP cc_start: 0.8605 (m-30) cc_final: 0.8254 (t0) REVERT: I 370 LYS cc_start: 0.7781 (tttm) cc_final: 0.7497 (tmtt) REVERT: I 373 THR cc_start: 0.8793 (m) cc_final: 0.8304 (p) REVERT: J 311 LYS cc_start: 0.5719 (tppt) cc_final: 0.5504 (tppt) REVERT: J 345 ASP cc_start: 0.8491 (m-30) cc_final: 0.8166 (t0) REVERT: J 353 LYS cc_start: 0.9268 (mtmt) cc_final: 0.8966 (mtmt) outliers start: 21 outliers final: 17 residues processed: 249 average time/residue: 0.4331 time to fit residues: 136.9375 Evaluate side-chains 247 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 230 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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 E residue 307 GLN 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 359 ASN Chi-restraints excluded: chain J residue 307 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 50 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 49 optimal weight: 0.0040 chunk 58 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 336 GLN ** E 359 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** I 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.159477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.140004 restraints weight = 27264.470| |-----------------------------------------------------------------------------| r_work (start): 0.4493 rms_B_bonded: 3.30 r_work: 0.4484 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.4370 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.8016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5660 Z= 0.135 Angle : 0.672 4.980 7580 Z= 0.325 Chirality : 0.048 0.148 860 Planarity : 0.006 0.051 960 Dihedral : 5.599 16.668 740 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.79 % Favored : 85.21 % Rotamer: Outliers : 3.59 % Allowed : 22.50 % 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: -5.74 (0.17), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.37 (0.13), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 330 PHE 0.005 0.001 PHE E 346 TYR 0.015 0.002 TYR A 310 ARG 0.004 0.000 ARG J 349 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 5660) covalent geometry : angle 0.67216 ( 7580) *********************** 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 256 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 233 time to evaluate : 0.855 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: A 349 ARG cc_start: 0.8694 (mtp180) cc_final: 0.8424 (mtp180) REVERT: A 372 GLU cc_start: 0.8120 (mp0) cc_final: 0.7636 (mp0) REVERT: B 353 LYS cc_start: 0.9162 (mtmt) cc_final: 0.8807 (mtpp) REVERT: B 358 ASP cc_start: 0.8900 (p0) cc_final: 0.8591 (p0) REVERT: B 376 LEU cc_start: 0.8360 (tp) cc_final: 0.8121 (tt) REVERT: D 345 ASP cc_start: 0.8101 (t0) cc_final: 0.7850 (t0) REVERT: D 358 ASP cc_start: 0.9029 (p0) cc_final: 0.8694 (p0) REVERT: E 358 ASP cc_start: 0.8786 (p0) cc_final: 0.8567 (p0) REVERT: F 345 ASP cc_start: 0.8376 (m-30) cc_final: 0.8123 (t0) REVERT: G 345 ASP cc_start: 0.8487 (m-30) cc_final: 0.7954 (t0) REVERT: H 342 GLU cc_start: 0.8208 (mp0) cc_final: 0.7841 (mp0) REVERT: I 307 GLN cc_start: 0.8246 (tt0) cc_final: 0.7267 (mp10) REVERT: I 345 ASP cc_start: 0.8554 (m-30) cc_final: 0.8314 (t0) REVERT: I 373 THR cc_start: 0.8810 (m) cc_final: 0.8300 (p) REVERT: J 340 LYS cc_start: 0.7693 (mmtt) cc_final: 0.7110 (mmmt) REVERT: J 345 ASP cc_start: 0.8501 (m-30) cc_final: 0.8214 (t0) REVERT: J 353 LYS cc_start: 0.9241 (mtmt) cc_final: 0.8917 (mtmt) REVERT: J 370 LYS cc_start: 0.8062 (ttmt) cc_final: 0.7642 (tttt) outliers start: 23 outliers final: 19 residues processed: 245 average time/residue: 0.4148 time to fit residues: 127.7930 Evaluate side-chains 244 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 225 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 307 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 F residue 325 LEU 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 359 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 55 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 56 optimal weight: 0.0070 chunk 60 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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** I 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.161237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.141901 restraints weight = 27066.710| |-----------------------------------------------------------------------------| r_work (start): 0.4543 rms_B_bonded: 3.30 r_work: 0.4536 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.4421 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.4421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.8132 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 : 0.667 4.897 7580 Z= 0.321 Chirality : 0.048 0.141 860 Planarity : 0.006 0.064 960 Dihedral : 5.435 17.035 740 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.77 % Favored : 84.23 % Rotamer: Outliers : 2.50 % Allowed : 24.53 % 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: -5.64 (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 0.004 0.001 HIS D 330 PHE 0.003 0.001 PHE E 346 TYR 0.013 0.002 TYR A 310 ARG 0.003 0.001 ARG J 349 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 5660) covalent geometry : angle 0.66750 ( 7580) ********************** 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 243 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 227 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.8332 (tt0) cc_final: 0.8075 (tm-30) REVERT: A 349 ARG cc_start: 0.8696 (mtp180) cc_final: 0.8394 (mtp180) REVERT: A 372 GLU cc_start: 0.8025 (mp0) cc_final: 0.7774 (mp0) REVERT: B 353 LYS cc_start: 0.9188 (mtmt) cc_final: 0.8811 (mtpp) REVERT: B 358 ASP cc_start: 0.8891 (p0) cc_final: 0.8600 (p0) REVERT: D 325 LEU cc_start: 0.7682 (mt) cc_final: 0.6976 (mt) REVERT: D 358 ASP cc_start: 0.9066 (p0) cc_final: 0.8735 (p0) REVERT: F 342 GLU cc_start: 0.8357 (mp0) cc_final: 0.7907 (mp0) REVERT: F 345 ASP cc_start: 0.8363 (m-30) cc_final: 0.8028 (t0) REVERT: G 345 ASP cc_start: 0.8448 (m-30) cc_final: 0.7857 (t0) REVERT: H 342 GLU cc_start: 0.8228 (mp0) cc_final: 0.7852 (mp0) REVERT: H 349 ARG cc_start: 0.7856 (mtp180) cc_final: 0.7279 (ttm110) REVERT: I 307 GLN cc_start: 0.8238 (tt0) cc_final: 0.7229 (mp10) REVERT: I 345 ASP cc_start: 0.8584 (m-30) cc_final: 0.8319 (t0) REVERT: I 373 THR cc_start: 0.8762 (m) cc_final: 0.8235 (p) REVERT: J 340 LYS cc_start: 0.7589 (mmtt) cc_final: 0.7006 (mmmt) REVERT: J 345 ASP cc_start: 0.8511 (m-30) cc_final: 0.8177 (t0) REVERT: J 353 LYS cc_start: 0.9193 (mtmt) cc_final: 0.8853 (mtmt) outliers start: 16 outliers final: 15 residues processed: 237 average time/residue: 0.4027 time to fit residues: 120.6465 Evaluate side-chains 240 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 225 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 E residue 307 GLN Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain F residue 325 LEU 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 I residue 336 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 23 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.4753 r_free = 0.4753 target = 0.161041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.141471 restraints weight = 26978.955| |-----------------------------------------------------------------------------| r_work (start): 0.4529 rms_B_bonded: 3.34 r_work: 0.4524 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.4410 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.4410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.8141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.244 5660 Z= 0.299 Angle : 1.091 59.167 7580 Z= 0.630 Chirality : 0.052 0.545 860 Planarity : 0.006 0.062 960 Dihedral : 5.435 17.027 740 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.34 % Favored : 83.66 % Rotamer: Outliers : 2.34 % Allowed : 24.53 % Favored : 73.12 % Cbeta Deviations : 0.16 % 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 : -4.28 (0.13), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 330 PHE 0.003 0.001 PHE I 378 TYR 0.012 0.002 TYR A 310 ARG 0.003 0.000 ARG F 349 Details of bonding type rmsd covalent geometry : bond 0.00594 ( 5660) covalent geometry : angle 1.09073 ( 7580) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7708.80 seconds wall clock time: 133 minutes 8.94 seconds (7988.94 seconds total)