Starting phenix.real_space_refine on Wed Sep 17 20:24:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5o3t_3743/09_2025/5o3t_3743.cif Found real_map, /net/cci-nas-00/data/ceres_data/5o3t_3743/09_2025/5o3t_3743.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/5o3t_3743/09_2025/5o3t_3743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5o3t_3743/09_2025/5o3t_3743.map" model { file = "/net/cci-nas-00/data/ceres_data/5o3t_3743/09_2025/5o3t_3743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5o3t_3743/09_2025/5o3t_3743.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 10 5.16 5 C 3510 2.51 5 N 1010 2.21 5 O 1040 1.98 5 H 5790 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.95, per 1000 atoms: 0.17 Number of scatterers: 11360 At special positions: 0 Unit cell: (116.48, 114.4, 46.8, 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: 1.09 Conformation dependent library (CDL) restraints added in 248.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.57 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: 1.44 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: 2130 1.41 - 1.60: 3520 1.60 - 1.79: 10 Bond restraints: 11450 Sorted by residual: bond pdb=" C VAL G 363 " pdb=" N PRO G 364 " ideal model delta sigma weight residual 1.334 1.319 0.015 1.11e-02 8.12e+03 1.89e+00 bond pdb=" C VAL F 363 " pdb=" N PRO F 364 " ideal model delta sigma weight residual 1.334 1.319 0.015 1.11e-02 8.12e+03 1.76e+00 bond pdb=" C VAL H 363 " pdb=" N PRO H 364 " ideal model delta sigma weight residual 1.334 1.319 0.014 1.11e-02 8.12e+03 1.70e+00 bond pdb=" C VAL C 363 " pdb=" N PRO C 364 " ideal model delta sigma weight residual 1.334 1.320 0.014 1.11e-02 8.12e+03 1.63e+00 bond pdb=" C VAL J 363 " pdb=" N PRO J 364 " ideal model delta sigma weight residual 1.334 1.320 0.014 1.11e-02 8.12e+03 1.54e+00 ... (remaining 11445 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 17684 1.56 - 3.12: 2803 3.12 - 4.69: 383 4.69 - 6.25: 10 6.25 - 7.81: 20 Bond angle restraints: 20900 Sorted by residual: angle pdb=" N LYS I 331 " pdb=" CA LYS I 331 " pdb=" C LYS I 331 " ideal model delta sigma weight residual 108.97 116.78 -7.81 1.82e+00 3.02e-01 1.84e+01 angle pdb=" N LYS E 331 " pdb=" CA LYS E 331 " pdb=" C LYS E 331 " ideal model delta sigma weight residual 108.97 116.78 -7.81 1.82e+00 3.02e-01 1.84e+01 angle pdb=" N LYS C 331 " pdb=" CA LYS C 331 " pdb=" C LYS C 331 " ideal model delta sigma weight residual 108.97 116.75 -7.78 1.82e+00 3.02e-01 1.83e+01 angle pdb=" N LYS A 331 " pdb=" CA LYS A 331 " pdb=" C LYS A 331 " ideal model delta sigma weight residual 108.97 116.75 -7.78 1.82e+00 3.02e-01 1.83e+01 angle pdb=" N LYS G 331 " pdb=" CA LYS G 331 " pdb=" C LYS G 331 " ideal model delta sigma weight residual 108.97 116.74 -7.77 1.82e+00 3.02e-01 1.82e+01 ... (remaining 20895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.52: 4578 10.52 - 21.04: 327 21.04 - 31.56: 195 31.56 - 42.09: 80 42.09 - 52.61: 90 Dihedral angle restraints: 5270 sinusoidal: 3000 harmonic: 2270 Sorted by residual: dihedral pdb=" CA LEU E 315 " pdb=" C LEU E 315 " pdb=" N SER E 316 " pdb=" CA SER E 316 " ideal model delta harmonic sigma weight residual 180.00 -157.61 -22.39 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA LEU F 315 " pdb=" C LEU F 315 " pdb=" N SER F 316 " pdb=" CA SER F 316 " ideal model delta harmonic sigma weight residual -180.00 -157.63 -22.37 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA LEU C 315 " pdb=" C LEU C 315 " pdb=" N SER C 316 " pdb=" CA SER C 316 " ideal model delta harmonic sigma weight residual -180.00 -157.64 -22.36 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 5267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 390 0.027 - 0.054: 216 0.054 - 0.081: 114 0.081 - 0.108: 78 0.108 - 0.135: 62 Chirality restraints: 860 Sorted by residual: chirality pdb=" CA LYS C 331 " pdb=" N LYS C 331 " pdb=" C LYS C 331 " pdb=" CB LYS C 331 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA ILE E 328 " pdb=" N ILE E 328 " pdb=" C ILE E 328 " pdb=" CB ILE E 328 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA ILE F 328 " pdb=" N ILE F 328 " pdb=" C ILE F 328 " pdb=" CB ILE F 328 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 857 not shown) Planarity restraints: 1650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 363 " -0.029 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO B 364 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 364 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 364 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 363 " -0.029 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO D 364 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 364 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 364 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 363 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO G 364 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO G 364 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 364 " -0.024 5.00e-02 4.00e+02 ... (remaining 1647 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.91: 171 1.91 - 2.58: 12948 2.58 - 3.26: 33858 3.26 - 3.93: 42845 3.93 - 4.60: 66195 Nonbonded interactions: 156017 Sorted by model distance: nonbonded pdb=" HB3 HIS F 329 " pdb=" HE3 LYS F 331 " model vdw 1.242 2.440 nonbonded pdb=" HB3 HIS B 329 " pdb=" HE3 LYS B 331 " model vdw 1.242 2.440 nonbonded pdb=" HB3 HIS J 329 " pdb=" HE3 LYS J 331 " model vdw 1.242 2.440 nonbonded pdb=" HB3 HIS D 329 " pdb=" HE3 LYS D 331 " model vdw 1.243 2.440 nonbonded pdb=" HB3 HIS H 329 " pdb=" HE3 LYS H 331 " model vdw 1.243 2.440 ... (remaining 156012 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: 0.03 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: 1.300 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: 0.070 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.410 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6093 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 : 0.007 0.053 5660 Z= 0.273 Angle : 0.915 7.811 7580 Z= 0.472 Chirality : 0.055 0.135 860 Planarity : 0.005 0.043 960 Dihedral : 10.151 50.514 2160 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.08 % Favored : 85.92 % Rotamer: Outliers : 1.56 % Allowed : 3.12 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.47 (0.15), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.93 (0.12), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG F 349 TYR 0.005 0.003 TYR C 310 PHE 0.007 0.001 PHE D 346 HIS 0.006 0.002 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00662 ( 5660) covalent geometry : angle 0.91542 ( 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 154 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 0.323 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: symmetry clash revert: symmetry clash REVERT: B 360 ILE cc_start: 0.6710 (mp) cc_final: 0.6455 (mt) REVERT: D 360 ILE cc_start: 0.5942 (mp) cc_final: 0.5684 (mt) REVERT: G 331 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7616 (mttt) outliers start: 10 outliers final: 5 residues processed: 154 average time/residue: 0.3048 time to fit residues: 54.7742 Evaluate side-chains 89 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain G residue 331 LYS Chi-restraints excluded: chain H residue 331 LYS Chi-restraints excluded: chain J residue 331 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 HIS G 351 GLN ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 336 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5063 r_free = 0.5063 target = 0.205431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.154649 restraints weight = 19588.039| |-----------------------------------------------------------------------------| r_work (start): 0.4670 rms_B_bonded: 3.25 r_work: 0.4556 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5660 Z= 0.183 Angle : 0.662 4.747 7580 Z= 0.341 Chirality : 0.052 0.147 860 Planarity : 0.004 0.028 960 Dihedral : 7.829 50.103 764 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.10 % Favored : 86.90 % Rotamer: Outliers : 1.56 % Allowed : 9.69 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.02 (0.17), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.58 (0.13), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG J 349 TYR 0.010 0.003 TYR I 310 PHE 0.021 0.002 PHE J 346 HIS 0.005 0.001 HIS D 329 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 5660) covalent geometry : angle 0.66178 ( 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 105 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.301 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 338 GLU cc_start: 0.6436 (tp30) cc_final: 0.5498 (tm-30) REVERT: A 345 ASP cc_start: 0.7292 (t0) cc_final: 0.6867 (t0) REVERT: A 347 LYS cc_start: 0.7959 (mttt) cc_final: 0.7687 (mttp) REVERT: A 369 LYS cc_start: 0.7817 (tttt) cc_final: 0.7414 (tttm) REVERT: B 331 LYS cc_start: 0.5966 (OUTLIER) cc_final: 0.4291 (mmtt) REVERT: C 338 GLU cc_start: 0.7008 (tp30) cc_final: 0.5345 (tp30) REVERT: C 347 LYS cc_start: 0.8120 (mttt) cc_final: 0.7873 (mttp) REVERT: D 338 GLU cc_start: 0.3641 (mp0) cc_final: 0.3224 (mp0) REVERT: E 338 GLU cc_start: 0.6614 (tp30) cc_final: 0.6293 (tp30) REVERT: G 338 GLU cc_start: 0.7031 (tp30) cc_final: 0.6820 (tp30) REVERT: G 353 LYS cc_start: 0.8040 (mtpp) cc_final: 0.7767 (ttpp) REVERT: G 357 LEU cc_start: 0.8852 (tt) cc_final: 0.8611 (tt) REVERT: G 369 LYS cc_start: 0.7623 (mtpt) cc_final: 0.7275 (mtpp) outliers start: 10 outliers final: 7 residues processed: 103 average time/residue: 0.2169 time to fit residues: 27.6885 Evaluate side-chains 85 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain J residue 331 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 11 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 362 HIS F 336 GLN F 359 ASN ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 362 HIS J 359 ASN J 368 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5039 r_free = 0.5039 target = 0.201315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.150393 restraints weight = 19815.142| |-----------------------------------------------------------------------------| r_work (start): 0.4640 rms_B_bonded: 3.07 r_work: 0.4537 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.4433 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.4433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5660 Z= 0.167 Angle : 0.601 3.910 7580 Z= 0.311 Chirality : 0.049 0.129 860 Planarity : 0.003 0.023 960 Dihedral : 7.175 51.995 752 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.97 % Favored : 88.03 % Rotamer: Outliers : 1.25 % Allowed : 12.19 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.75 (0.19), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.38 (0.14), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 349 TYR 0.009 0.002 TYR C 310 PHE 0.016 0.002 PHE J 346 HIS 0.005 0.001 HIS I 330 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 5660) covalent geometry : angle 0.60143 ( 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 100 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.6473 (tp30) cc_final: 0.5562 (tm-30) REVERT: A 345 ASP cc_start: 0.7412 (t0) cc_final: 0.6901 (t0) REVERT: A 347 LYS cc_start: 0.7978 (mttt) cc_final: 0.7643 (mttp) REVERT: C 356 SER cc_start: 0.8267 (t) cc_final: 0.7820 (m) REVERT: G 353 LYS cc_start: 0.8136 (mtpp) cc_final: 0.7822 (ttpp) REVERT: G 357 LEU cc_start: 0.8809 (tt) cc_final: 0.8504 (tt) REVERT: J 368 ASN cc_start: 0.7595 (m110) cc_final: 0.7257 (m-40) outliers start: 8 outliers final: 6 residues processed: 98 average time/residue: 0.1931 time to fit residues: 24.1874 Evaluate side-chains 85 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain J residue 331 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 31 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 58 optimal weight: 0.1980 chunk 26 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 HIS D 362 HIS F 362 HIS ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 362 HIS ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 362 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5001 r_free = 0.5001 target = 0.195404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.142690 restraints weight = 19906.755| |-----------------------------------------------------------------------------| r_work (start): 0.4554 rms_B_bonded: 3.12 r_work: 0.4462 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.5830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5660 Z= 0.185 Angle : 0.597 3.735 7580 Z= 0.309 Chirality : 0.050 0.136 860 Planarity : 0.003 0.028 960 Dihedral : 7.087 54.729 748 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.25 % Favored : 87.75 % Rotamer: Outliers : 2.03 % Allowed : 13.91 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.55 (0.20), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.22 (0.15), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 349 TYR 0.010 0.003 TYR E 310 PHE 0.017 0.002 PHE J 346 HIS 0.006 0.002 HIS I 330 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 5660) covalent geometry : angle 0.59679 ( 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 105 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.346 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 369 LYS cc_start: 0.7954 (tttt) cc_final: 0.7577 (tttm) REVERT: B 331 LYS cc_start: 0.6426 (OUTLIER) cc_final: 0.4207 (mmtm) REVERT: C 353 LYS cc_start: 0.7962 (ttpp) cc_final: 0.7536 (tttt) REVERT: D 354 ILE cc_start: 0.7267 (mt) cc_final: 0.7001 (mm) REVERT: F 354 ILE cc_start: 0.7156 (mt) cc_final: 0.6927 (mm) REVERT: G 353 LYS cc_start: 0.8087 (mtpp) cc_final: 0.7788 (ttpp) REVERT: G 357 LEU cc_start: 0.8863 (tt) cc_final: 0.8516 (tt) REVERT: G 369 LYS cc_start: 0.7930 (ttpt) cc_final: 0.7720 (tttt) REVERT: J 368 ASN cc_start: 0.7366 (m110) cc_final: 0.7151 (m-40) outliers start: 13 outliers final: 9 residues processed: 100 average time/residue: 0.2332 time to fit residues: 29.1706 Evaluate side-chains 83 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain J residue 331 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 37 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 HIS ** 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 = 0.4978 r_free = 0.4978 target = 0.181625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.130726 restraints weight = 19520.607| |-----------------------------------------------------------------------------| r_work (start): 0.4473 rms_B_bonded: 3.01 r_work: 0.4386 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.4275 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.6444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5660 Z= 0.180 Angle : 0.582 3.857 7580 Z= 0.300 Chirality : 0.050 0.149 860 Planarity : 0.003 0.031 960 Dihedral : 7.063 56.865 748 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.24 % Favored : 86.76 % Rotamer: Outliers : 1.88 % Allowed : 15.16 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.45 (0.20), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.14 (0.15), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 349 TYR 0.010 0.003 TYR E 310 PHE 0.011 0.001 PHE A 346 HIS 0.005 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 5660) covalent geometry : angle 0.58162 ( 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 100 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.6367 (OUTLIER) cc_final: 0.4181 (mmtm) REVERT: C 338 GLU cc_start: 0.6903 (tp30) cc_final: 0.6547 (tp30) REVERT: D 354 ILE cc_start: 0.7190 (mt) cc_final: 0.6956 (mm) REVERT: E 342 GLU cc_start: 0.7007 (mp0) cc_final: 0.6756 (mp0) REVERT: F 354 ILE cc_start: 0.7238 (mt) cc_final: 0.6971 (mm) REVERT: G 338 GLU cc_start: 0.7026 (tp30) cc_final: 0.6815 (tm-30) REVERT: G 353 LYS cc_start: 0.7874 (mtpp) cc_final: 0.7574 (ttpp) REVERT: G 357 LEU cc_start: 0.8798 (tt) cc_final: 0.8442 (tt) REVERT: I 346 PHE cc_start: 0.7795 (m-10) cc_final: 0.7574 (m-10) REVERT: J 354 ILE cc_start: 0.7297 (mm) cc_final: 0.7061 (tp) REVERT: J 368 ASN cc_start: 0.7506 (m110) cc_final: 0.7228 (m-40) outliers start: 12 outliers final: 10 residues processed: 97 average time/residue: 0.1957 time to fit residues: 24.7439 Evaluate side-chains 91 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain J residue 331 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 60 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 329 HIS ** 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 = 0.5004 r_free = 0.5004 target = 0.182798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.131924 restraints weight = 19338.343| |-----------------------------------------------------------------------------| r_work (start): 0.4504 rms_B_bonded: 3.02 r_work: 0.4421 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.4315 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.4315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.6777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5660 Z= 0.136 Angle : 0.547 3.735 7580 Z= 0.281 Chirality : 0.049 0.129 860 Planarity : 0.003 0.030 960 Dihedral : 6.828 58.413 748 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.13 % Favored : 88.87 % Rotamer: Outliers : 1.72 % Allowed : 15.78 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.32 (0.20), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.05 (0.15), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 349 TYR 0.010 0.002 TYR E 310 PHE 0.010 0.001 PHE A 346 HIS 0.004 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 5660) covalent geometry : angle 0.54705 ( 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 91 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.6359 (OUTLIER) cc_final: 0.4171 (mmtm) REVERT: C 338 GLU cc_start: 0.6927 (tp30) cc_final: 0.6539 (tp30) REVERT: D 354 ILE cc_start: 0.7202 (mt) cc_final: 0.6960 (mm) REVERT: E 342 GLU cc_start: 0.6881 (mp0) cc_final: 0.6608 (mp0) REVERT: F 354 ILE cc_start: 0.7314 (mt) cc_final: 0.7024 (mm) REVERT: G 353 LYS cc_start: 0.7906 (mtpp) cc_final: 0.7550 (ttpp) REVERT: G 357 LEU cc_start: 0.8802 (tt) cc_final: 0.8468 (tt) REVERT: I 346 PHE cc_start: 0.7820 (m-10) cc_final: 0.7363 (m-10) REVERT: J 354 ILE cc_start: 0.7332 (mm) cc_final: 0.7078 (tp) outliers start: 11 outliers final: 10 residues processed: 88 average time/residue: 0.2044 time to fit residues: 23.2033 Evaluate side-chains 84 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain J residue 331 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 329 HIS ** 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 = 0.4959 r_free = 0.4959 target = 0.178139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.128349 restraints weight = 19626.698| |-----------------------------------------------------------------------------| r_work (start): 0.4443 rms_B_bonded: 2.94 r_work: 0.4355 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.4245 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.4245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.7106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5660 Z= 0.193 Angle : 0.578 4.113 7580 Z= 0.298 Chirality : 0.050 0.130 860 Planarity : 0.003 0.030 960 Dihedral : 7.008 59.670 748 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.37 % Favored : 85.63 % Rotamer: Outliers : 1.88 % Allowed : 15.94 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.26 (0.20), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.00 (0.16), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 349 TYR 0.010 0.003 TYR E 310 PHE 0.014 0.001 PHE A 346 HIS 0.006 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 5660) covalent geometry : angle 0.57751 ( 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 96 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.6468 (OUTLIER) cc_final: 0.4495 (mmtt) REVERT: C 338 GLU cc_start: 0.6983 (tp30) cc_final: 0.6576 (tp30) REVERT: E 342 GLU cc_start: 0.7024 (mp0) cc_final: 0.6717 (mp0) REVERT: F 354 ILE cc_start: 0.7366 (mt) cc_final: 0.7018 (mm) REVERT: G 338 GLU cc_start: 0.7156 (tp30) cc_final: 0.6885 (tm-30) REVERT: G 346 PHE cc_start: 0.7493 (m-10) cc_final: 0.7227 (m-10) REVERT: G 353 LYS cc_start: 0.7861 (mtpp) cc_final: 0.7524 (ttpp) REVERT: G 357 LEU cc_start: 0.8824 (tt) cc_final: 0.8519 (tt) REVERT: I 346 PHE cc_start: 0.7869 (m-10) cc_final: 0.7400 (m-10) REVERT: J 354 ILE cc_start: 0.7267 (mm) cc_final: 0.7053 (tp) outliers start: 12 outliers final: 11 residues processed: 93 average time/residue: 0.1964 time to fit residues: 23.6206 Evaluate side-chains 92 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain J residue 331 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 6 optimal weight: 0.1980 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 52 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 329 HIS ** 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 = 0.4993 r_free = 0.4993 target = 0.180946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.130807 restraints weight = 19379.396| |-----------------------------------------------------------------------------| r_work (start): 0.4492 rms_B_bonded: 3.03 r_work: 0.4409 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.4303 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.4303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.7276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5660 Z= 0.128 Angle : 0.538 3.982 7580 Z= 0.276 Chirality : 0.049 0.141 860 Planarity : 0.003 0.029 960 Dihedral : 6.702 58.478 748 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 1.88 % Allowed : 15.94 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.16 (0.20), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.15), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.010 0.002 TYR A 310 PHE 0.015 0.001 PHE E 346 HIS 0.004 0.001 HIS G 330 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 5660) covalent geometry : angle 0.53793 ( 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 93 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.6781 (OUTLIER) cc_final: 0.4438 (mmtm) REVERT: C 338 GLU cc_start: 0.7025 (tp30) cc_final: 0.6621 (tp30) REVERT: E 342 GLU cc_start: 0.7083 (mp0) cc_final: 0.6800 (mp0) REVERT: G 338 GLU cc_start: 0.7093 (tp30) cc_final: 0.6853 (tm-30) REVERT: G 353 LYS cc_start: 0.7808 (mtpp) cc_final: 0.7460 (ttpp) REVERT: G 357 LEU cc_start: 0.8857 (tt) cc_final: 0.8558 (tt) REVERT: I 346 PHE cc_start: 0.7900 (m-10) cc_final: 0.7488 (m-10) REVERT: J 354 ILE cc_start: 0.7341 (mm) cc_final: 0.7127 (tp) REVERT: J 370 LYS cc_start: 0.7837 (tttp) cc_final: 0.7056 (tppt) outliers start: 12 outliers final: 9 residues processed: 90 average time/residue: 0.2073 time to fit residues: 24.0663 Evaluate side-chains 83 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain J residue 331 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 7 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 65 optimal weight: 0.0870 chunk 10 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** 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 = 0.5001 r_free = 0.5001 target = 0.181314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.131376 restraints weight = 19374.750| |-----------------------------------------------------------------------------| r_work (start): 0.4496 rms_B_bonded: 3.02 r_work: 0.4407 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.4293 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.4293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.7381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5660 Z= 0.123 Angle : 0.530 4.921 7580 Z= 0.272 Chirality : 0.049 0.140 860 Planarity : 0.003 0.027 960 Dihedral : 6.445 56.849 748 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.82 % Favored : 87.18 % Rotamer: Outliers : 1.88 % Allowed : 16.41 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.05 (0.20), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.15), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 349 TYR 0.009 0.002 TYR I 310 PHE 0.016 0.001 PHE E 346 HIS 0.004 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 5660) covalent geometry : angle 0.52986 ( 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 91 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.6804 (OUTLIER) cc_final: 0.4505 (mmtm) REVERT: C 338 GLU cc_start: 0.6984 (tp30) cc_final: 0.6578 (tp30) REVERT: D 338 GLU cc_start: 0.4569 (mp0) cc_final: 0.4361 (mp0) REVERT: E 342 GLU cc_start: 0.7036 (mp0) cc_final: 0.6776 (mp0) REVERT: G 338 GLU cc_start: 0.7065 (tp30) cc_final: 0.6811 (tm-30) REVERT: G 346 PHE cc_start: 0.7430 (m-10) cc_final: 0.7126 (m-10) REVERT: G 353 LYS cc_start: 0.7720 (mtpp) cc_final: 0.7374 (ttpp) REVERT: G 357 LEU cc_start: 0.8836 (tt) cc_final: 0.8547 (tt) REVERT: I 346 PHE cc_start: 0.7884 (m-10) cc_final: 0.7319 (m-10) REVERT: J 354 ILE cc_start: 0.7316 (mm) cc_final: 0.7074 (tp) REVERT: J 370 LYS cc_start: 0.7758 (tttp) cc_final: 0.7122 (tppt) outliers start: 12 outliers final: 10 residues processed: 88 average time/residue: 0.2048 time to fit residues: 23.3184 Evaluate side-chains 85 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain I residue 356 SER Chi-restraints excluded: chain J residue 331 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 23 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 0.0270 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 41 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN ** F 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 = 0.4998 r_free = 0.4998 target = 0.180282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.130211 restraints weight = 19530.997| |-----------------------------------------------------------------------------| r_work (start): 0.4486 rms_B_bonded: 3.03 r_work: 0.4394 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.4282 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.7559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5660 Z= 0.140 Angle : 0.543 4.674 7580 Z= 0.279 Chirality : 0.049 0.141 860 Planarity : 0.003 0.025 960 Dihedral : 6.267 55.283 744 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.25 % Favored : 87.75 % Rotamer: Outliers : 1.56 % Allowed : 17.34 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.02 (0.20), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.16), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 349 TYR 0.009 0.002 TYR A 310 PHE 0.018 0.002 PHE E 346 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 5660) covalent geometry : angle 0.54318 ( 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 91 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.343 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: B 331 LYS cc_start: 0.6833 (OUTLIER) cc_final: 0.4533 (mmtm) REVERT: C 338 GLU cc_start: 0.7076 (tp30) cc_final: 0.6657 (tp30) REVERT: E 342 GLU cc_start: 0.7063 (mp0) cc_final: 0.6684 (mp0) REVERT: G 338 GLU cc_start: 0.7167 (tp30) cc_final: 0.6882 (tm-30) REVERT: G 346 PHE cc_start: 0.7392 (m-10) cc_final: 0.7083 (m-10) REVERT: G 353 LYS cc_start: 0.7705 (mtpp) cc_final: 0.7366 (ttpp) REVERT: G 357 LEU cc_start: 0.8880 (tt) cc_final: 0.8610 (tt) REVERT: I 346 PHE cc_start: 0.7878 (m-10) cc_final: 0.7433 (m-10) REVERT: J 354 ILE cc_start: 0.7298 (mm) cc_final: 0.7022 (tp) REVERT: J 370 LYS cc_start: 0.7769 (tttp) cc_final: 0.7165 (tppt) outliers start: 10 outliers final: 8 residues processed: 89 average time/residue: 0.2000 time to fit residues: 23.0321 Evaluate side-chains 89 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain I residue 356 SER Chi-restraints excluded: chain J residue 331 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 5 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 329 HIS ** 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 = 0.4982 r_free = 0.4982 target = 0.178325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.128750 restraints weight = 19688.117| |-----------------------------------------------------------------------------| r_work (start): 0.4472 rms_B_bonded: 3.05 r_work: 0.4383 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.4275 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.7710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5660 Z= 0.158 Angle : 0.551 4.484 7580 Z= 0.283 Chirality : 0.049 0.136 860 Planarity : 0.003 0.026 960 Dihedral : 6.299 53.343 744 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.94 % Favored : 86.06 % Rotamer: Outliers : 1.56 % Allowed : 17.66 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.98 (0.21), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.16), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 349 TYR 0.009 0.002 TYR A 310 PHE 0.017 0.001 PHE E 346 HIS 0.005 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 5660) covalent geometry : angle 0.55125 ( 7580) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3724.67 seconds wall clock time: 64 minutes 24.55 seconds (3864.55 seconds total)