Starting phenix.real_space_refine on Wed Mar 4 06:43:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wcb_21605/03_2026/6wcb_21605.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wcb_21605/03_2026/6wcb_21605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wcb_21605/03_2026/6wcb_21605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wcb_21605/03_2026/6wcb_21605.map" model { file = "/net/cci-nas-00/data/ceres_data/6wcb_21605/03_2026/6wcb_21605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wcb_21605/03_2026/6wcb_21605.cif" } resolution = 3.17 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 ------------------------------------------------------------------------------- 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= 1.000 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: 6 Type Number sf(0) Gaussians Cs 7 16.47 5 S 38 5.16 5 C 3754 2.51 5 N 938 2.21 5 O 1006 1.98 5 H 5904 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11647 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5800 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5800 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CS': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CS': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Time building chain proxies: 2.25, per 1000 atoms: 0.19 Number of scatterers: 11647 At special positions: 0 Unit cell: (105.536, 72.896, 77.248, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cs 7 54.66 S 38 16.00 O 1006 8.00 N 938 7.00 C 3754 6.00 H 5904 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: 1.01 Conformation dependent library (CDL) restraints added in 339.0 milliseconds 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1404 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 0 sheets defined 87.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 33 through 49 Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 66 through 102 Processing helix chain 'A' and resid 106 through 121 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 137 through 164 Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 257 through 284 removed outlier: 5.074A pdb=" N LEU A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ILE A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.642A pdb=" N ALA A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 332 Processing helix chain 'A' and resid 338 through 353 Processing helix chain 'A' and resid 354 through 364 Processing helix chain 'A' and resid 368 through 400 removed outlier: 3.798A pdb=" N GLU A 372 " --> pdb=" O GLN A 368 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 373 " --> pdb=" O PRO A 369 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N HIS A 400 " --> pdb=" O THR A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.585A pdb=" N TRP A 410 " --> pdb=" O PRO A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 439 removed outlier: 5.239A pdb=" N TYR A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Proline residue: A 427 - end of helix Processing helix chain 'A' and resid 443 through 461 Proline residue: A 456 - end of helix Processing helix chain 'A' and resid 461 through 507 Processing helix chain 'B' and resid 33 through 49 Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 66 through 102 Processing helix chain 'B' and resid 106 through 121 Processing helix chain 'B' and resid 122 through 133 Processing helix chain 'B' and resid 137 through 164 Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 257 through 284 removed outlier: 5.074A pdb=" N LEU B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ILE B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.643A pdb=" N ALA B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 331 Processing helix chain 'B' and resid 338 through 353 Processing helix chain 'B' and resid 354 through 364 Processing helix chain 'B' and resid 368 through 400 removed outlier: 3.797A pdb=" N GLU B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 373 " --> pdb=" O PRO B 369 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N HIS B 400 " --> pdb=" O THR B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 405 Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.583A pdb=" N TRP B 410 " --> pdb=" O PRO B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 439 removed outlier: 5.238A pdb=" N TYR B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Proline residue: B 427 - end of helix Processing helix chain 'B' and resid 443 through 461 Proline residue: B 456 - end of helix Processing helix chain 'B' and resid 461 through 475 465 hydrogen bonds defined for protein. 1383 hydrogen bond angles 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: 2.44 Time building geometry restraints manager: 1.42 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: 5886 1.03 - 1.23: 18 1.23 - 1.42: 2380 1.42 - 1.61: 3392 1.61 - 1.81: 58 Bond restraints: 11734 Sorted by residual: bond pdb=" C THR B 472 " pdb=" N LEU B 473 " ideal model delta sigma weight residual 1.335 1.550 -0.215 1.38e-02 5.25e+03 2.43e+02 bond pdb=" C THR A 472 " pdb=" N LEU A 505 " ideal model delta sigma weight residual 1.335 1.550 -0.215 1.38e-02 5.25e+03 2.43e+02 bond pdb=" C THR B 306 " pdb=" N GLY B 307 " ideal model delta sigma weight residual 1.340 1.330 0.010 6.60e-03 2.30e+04 2.49e+00 bond pdb=" C THR A 306 " pdb=" N GLY A 307 " ideal model delta sigma weight residual 1.340 1.330 0.010 6.60e-03 2.30e+04 2.40e+00 bond pdb=" CA GLY B 307 " pdb=" C GLY B 307 " ideal model delta sigma weight residual 1.511 1.517 -0.006 6.90e-03 2.10e+04 7.80e-01 ... (remaining 11729 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.87: 18993 0.87 - 1.73: 2174 1.73 - 2.60: 69 2.60 - 3.47: 20 3.47 - 4.34: 12 Bond angle restraints: 21268 Sorted by residual: angle pdb=" CA GLY A 307 " pdb=" C GLY A 307 " pdb=" N PRO A 308 " ideal model delta sigma weight residual 119.27 117.28 1.99 8.50e-01 1.38e+00 5.49e+00 angle pdb=" CA GLY B 307 " pdb=" C GLY B 307 " pdb=" N PRO B 308 " ideal model delta sigma weight residual 119.27 117.30 1.97 8.50e-01 1.38e+00 5.37e+00 angle pdb=" CA GLY A 307 " pdb=" C GLY A 307 " pdb=" O GLY A 307 " ideal model delta sigma weight residual 119.65 121.03 -1.38 6.70e-01 2.23e+00 4.27e+00 angle pdb=" CA GLY B 307 " pdb=" C GLY B 307 " pdb=" O GLY B 307 " ideal model delta sigma weight residual 119.65 121.01 -1.36 6.70e-01 2.23e+00 4.11e+00 angle pdb=" N ARG B 442 " pdb=" CA ARG B 442 " pdb=" C ARG B 442 " ideal model delta sigma weight residual 113.18 110.75 2.43 1.33e+00 5.65e-01 3.33e+00 ... (remaining 21263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.97: 4937 14.97 - 29.94: 399 29.94 - 44.92: 97 44.92 - 59.89: 89 59.89 - 74.86: 6 Dihedral angle restraints: 5528 sinusoidal: 2936 harmonic: 2592 Sorted by residual: dihedral pdb=" CA PHE B 99 " pdb=" C PHE B 99 " pdb=" N GLN B 100 " pdb=" CA GLN B 100 " ideal model delta harmonic sigma weight residual 180.00 164.56 15.44 0 5.00e+00 4.00e-02 9.54e+00 dihedral pdb=" CA PHE A 99 " pdb=" C PHE A 99 " pdb=" N GLN A 100 " pdb=" CA GLN A 100 " ideal model delta harmonic sigma weight residual 180.00 164.62 15.38 0 5.00e+00 4.00e-02 9.47e+00 dihedral pdb=" CB MET B 51 " pdb=" CG MET B 51 " pdb=" SD MET B 51 " pdb=" CE MET B 51 " ideal model delta sinusoidal sigma weight residual 180.00 123.83 56.17 3 1.50e+01 4.44e-03 9.39e+00 ... (remaining 5525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 666 0.024 - 0.047: 159 0.047 - 0.071: 91 0.071 - 0.095: 48 0.095 - 0.119: 14 Chirality restraints: 978 Sorted by residual: chirality pdb=" CA VAL B 285 " pdb=" N VAL B 285 " pdb=" C VAL B 285 " pdb=" CB VAL B 285 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.51e-01 chirality pdb=" CA VAL A 102 " pdb=" N VAL A 102 " pdb=" C VAL A 102 " pdb=" CB VAL A 102 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.48e-01 chirality pdb=" CA VAL A 285 " pdb=" N VAL A 285 " pdb=" C VAL A 285 " pdb=" CB VAL A 285 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.28e-01 ... (remaining 975 not shown) Planarity restraints: 1672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 420 " -0.005 2.00e-02 2.50e+03 9.58e-03 2.75e+00 pdb=" CG PHE A 420 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE A 420 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 420 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE A 420 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 420 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 420 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE A 420 " -0.004 2.00e-02 2.50e+03 pdb=" HD2 PHE A 420 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE A 420 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE A 420 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE A 420 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 420 " -0.010 2.00e-02 2.50e+03 9.16e-03 2.52e+00 pdb=" CG PHE B 420 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE B 420 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 420 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE B 420 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 420 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 420 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE B 420 " 0.003 2.00e-02 2.50e+03 pdb=" HD2 PHE B 420 " 0.004 2.00e-02 2.50e+03 pdb=" HE1 PHE B 420 " -0.005 2.00e-02 2.50e+03 pdb=" HE2 PHE B 420 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE B 420 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 307 " -0.015 5.00e-02 4.00e+02 2.19e-02 7.71e-01 pdb=" N PRO B 308 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO B 308 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 308 " -0.012 5.00e-02 4.00e+02 ... (remaining 1669 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.45: 6508 2.45 - 3.30: 44661 3.30 - 4.15: 61665 4.15 - 5.01: 110976 5.01 - 5.86: 148706 Nonbonded interactions: 372516 Sorted by model distance: nonbonded pdb=" HH TYR A 359 " pdb=" OE1 GLN A 452 " model vdw 1.596 2.450 nonbonded pdb=" HH TYR B 359 " pdb=" OE1 GLN B 452 " model vdw 1.597 2.450 nonbonded pdb=" HG1 THR A 319 " pdb=" OH TYR A 359 " model vdw 1.606 2.450 nonbonded pdb=" HE2 HIS B 95 " pdb=" OD1 ASN B 113 " model vdw 1.617 2.450 nonbonded pdb=" HE2 HIS A 95 " pdb=" OD1 ASN A 113 " model vdw 1.617 2.450 ... (remaining 372511 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 30 through 703) selection = chain 'B' } 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: 0.010 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.280 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 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 : 0.005 0.215 5830 Z= 0.310 Angle : 0.414 4.336 7946 Z= 0.240 Chirality : 0.033 0.119 978 Planarity : 0.003 0.022 974 Dihedral : 13.865 74.862 2034 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.29 % Allowed : 6.80 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.30), residues: 726 helix: 1.01 (0.21), residues: 595 sheet: None (None), residues: 0 loop : -2.39 (0.50), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 370 TYR 0.004 0.001 TYR B 313 PHE 0.025 0.001 PHE A 420 TRP 0.005 0.001 TRP A 394 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 5830) covalent geometry : angle 0.41400 ( 7946) hydrogen bonds : bond 0.11405 ( 465) hydrogen bonds : angle 4.57285 ( 1383) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 0.252 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 34 GLN cc_start: 0.7772 (tt0) cc_final: 0.7483 (tt0) REVERT: A 339 ARG cc_start: 0.6755 (tpt170) cc_final: 0.5836 (ttm-80) REVERT: A 451 MET cc_start: 0.7484 (mmt) cc_final: 0.7222 (ttt) REVERT: B 34 GLN cc_start: 0.7839 (tt0) cc_final: 0.7522 (tt0) REVERT: B 339 ARG cc_start: 0.6756 (tpt170) cc_final: 0.5742 (ttm-80) REVERT: B 451 MET cc_start: 0.7501 (mmt) cc_final: 0.7167 (ttt) outliers start: 8 outliers final: 4 residues processed: 139 average time/residue: 0.1632 time to fit residues: 29.9911 Evaluate side-chains 115 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 316 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.166346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.120398 restraints weight = 8362.520| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.27 r_work: 0.3023 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 5830 Z= 0.209 Angle : 0.531 5.430 7946 Z= 0.282 Chirality : 0.038 0.120 978 Planarity : 0.004 0.037 974 Dihedral : 5.139 54.138 784 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.62 % Allowed : 10.03 % Favored : 88.35 % 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 are not related in a simple way. whole: 1.67 (0.31), residues: 726 helix: 1.73 (0.21), residues: 597 sheet: None (None), residues: 0 loop : -1.91 (0.53), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 260 TYR 0.011 0.002 TYR B 359 PHE 0.014 0.002 PHE A 389 TRP 0.010 0.002 TRP B 324 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 5830) covalent geometry : angle 0.53104 ( 7946) hydrogen bonds : bond 0.04494 ( 465) hydrogen bonds : angle 3.91844 ( 1383) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8314 (tt0) cc_final: 0.7801 (tt0) REVERT: A 131 VAL cc_start: 0.8302 (OUTLIER) cc_final: 0.8073 (t) REVERT: A 259 GLU cc_start: 0.7976 (mp0) cc_final: 0.7706 (mp0) REVERT: A 339 ARG cc_start: 0.6885 (tpt170) cc_final: 0.6081 (mtp85) REVERT: A 362 THR cc_start: 0.8216 (m) cc_final: 0.7955 (p) REVERT: A 451 MET cc_start: 0.7745 (mmt) cc_final: 0.6898 (ttt) REVERT: B 34 GLN cc_start: 0.8323 (tt0) cc_final: 0.7950 (tt0) REVERT: B 131 VAL cc_start: 0.8236 (OUTLIER) cc_final: 0.7978 (t) REVERT: B 259 GLU cc_start: 0.8049 (mp0) cc_final: 0.7814 (mp0) REVERT: B 339 ARG cc_start: 0.6821 (tpt170) cc_final: 0.5663 (ttm-80) REVERT: B 362 THR cc_start: 0.8168 (m) cc_final: 0.7936 (p) REVERT: B 451 MET cc_start: 0.7723 (mmt) cc_final: 0.6881 (ttt) outliers start: 10 outliers final: 8 residues processed: 132 average time/residue: 0.2202 time to fit residues: 36.0596 Evaluate side-chains 134 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 363 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.164619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.117466 restraints weight = 8637.837| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.34 r_work: 0.3023 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 5830 Z= 0.122 Angle : 0.450 4.231 7946 Z= 0.237 Chirality : 0.035 0.140 978 Planarity : 0.003 0.025 974 Dihedral : 4.902 51.397 784 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 1.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.62 % Allowed : 11.49 % Favored : 86.89 % 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 are not related in a simple way. whole: 2.37 (0.32), residues: 726 helix: 2.15 (0.21), residues: 603 sheet: None (None), residues: 0 loop : -1.47 (0.57), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 309 TYR 0.010 0.001 TYR B 359 PHE 0.008 0.001 PHE A 99 TRP 0.007 0.001 TRP A 394 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 5830) covalent geometry : angle 0.44968 ( 7946) hydrogen bonds : bond 0.04079 ( 465) hydrogen bonds : angle 3.68381 ( 1383) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8294 (tt0) cc_final: 0.7750 (tt0) REVERT: A 131 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.8104 (t) REVERT: A 339 ARG cc_start: 0.6898 (tpt170) cc_final: 0.6105 (mtp85) REVERT: A 451 MET cc_start: 0.7679 (mmt) cc_final: 0.6853 (ttt) REVERT: B 34 GLN cc_start: 0.8329 (tt0) cc_final: 0.7968 (tt0) REVERT: B 131 VAL cc_start: 0.8309 (OUTLIER) cc_final: 0.8071 (t) REVERT: B 259 GLU cc_start: 0.8061 (mp0) cc_final: 0.7780 (mp0) REVERT: B 339 ARG cc_start: 0.6811 (tpt170) cc_final: 0.6087 (mtp85) REVERT: B 451 MET cc_start: 0.7737 (mmt) cc_final: 0.6907 (ttt) outliers start: 10 outliers final: 6 residues processed: 140 average time/residue: 0.2126 time to fit residues: 36.9017 Evaluate side-chains 135 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 336 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 37 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 14 optimal weight: 0.0970 chunk 24 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 overall best weight: 3.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.163861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.118156 restraints weight = 8636.896| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.26 r_work: 0.3028 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5830 Z= 0.135 Angle : 0.456 4.267 7946 Z= 0.243 Chirality : 0.035 0.128 978 Planarity : 0.003 0.023 974 Dihedral : 4.784 50.696 784 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.29 % Allowed : 12.62 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.76 (0.32), residues: 726 helix: 2.44 (0.21), residues: 597 sheet: None (None), residues: 0 loop : -1.23 (0.56), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 260 TYR 0.011 0.002 TYR A 359 PHE 0.009 0.001 PHE A 99 TRP 0.006 0.001 TRP B 394 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 5830) covalent geometry : angle 0.45618 ( 7946) hydrogen bonds : bond 0.03950 ( 465) hydrogen bonds : angle 3.62860 ( 1383) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8257 (tt0) cc_final: 0.7721 (tt0) REVERT: A 131 VAL cc_start: 0.8307 (OUTLIER) cc_final: 0.8093 (t) REVERT: A 259 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7683 (mt-10) REVERT: A 339 ARG cc_start: 0.6912 (tpt170) cc_final: 0.6107 (mtp85) REVERT: A 451 MET cc_start: 0.7652 (mmt) cc_final: 0.6849 (ttt) REVERT: B 34 GLN cc_start: 0.8285 (tt0) cc_final: 0.7900 (tt0) REVERT: B 131 VAL cc_start: 0.8295 (OUTLIER) cc_final: 0.8059 (t) REVERT: B 339 ARG cc_start: 0.6837 (tpt170) cc_final: 0.6109 (mtp85) REVERT: B 451 MET cc_start: 0.7661 (mmt) cc_final: 0.6870 (ttt) outliers start: 8 outliers final: 5 residues processed: 140 average time/residue: 0.2061 time to fit residues: 36.0033 Evaluate side-chains 141 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 336 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 54 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.162733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.116563 restraints weight = 8680.043| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.28 r_work: 0.2988 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 5830 Z= 0.134 Angle : 0.457 4.242 7946 Z= 0.242 Chirality : 0.035 0.174 978 Planarity : 0.003 0.024 974 Dihedral : 4.568 49.256 784 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.29 % Allowed : 12.94 % Favored : 85.76 % 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 are not related in a simple way. whole: 3.00 (0.32), residues: 726 helix: 2.58 (0.21), residues: 597 sheet: None (None), residues: 0 loop : -0.99 (0.58), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 260 TYR 0.010 0.002 TYR B 359 PHE 0.009 0.001 PHE A 389 TRP 0.006 0.001 TRP B 394 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 5830) covalent geometry : angle 0.45718 ( 7946) hydrogen bonds : bond 0.03895 ( 465) hydrogen bonds : angle 3.59487 ( 1383) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8232 (tt0) cc_final: 0.7696 (tt0) REVERT: A 104 LYS cc_start: 0.7772 (mttt) cc_final: 0.7523 (mtpp) REVERT: A 259 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7700 (mt-10) REVERT: A 339 ARG cc_start: 0.6937 (tpt170) cc_final: 0.6129 (mtp85) REVERT: A 451 MET cc_start: 0.7690 (mmt) cc_final: 0.6897 (ttt) REVERT: B 34 GLN cc_start: 0.8281 (tt0) cc_final: 0.7879 (tt0) REVERT: B 131 VAL cc_start: 0.8275 (OUTLIER) cc_final: 0.8048 (t) REVERT: B 339 ARG cc_start: 0.6815 (tpt170) cc_final: 0.6067 (mtp85) REVERT: B 451 MET cc_start: 0.7647 (mmt) cc_final: 0.6865 (ttt) outliers start: 8 outliers final: 2 residues processed: 137 average time/residue: 0.1970 time to fit residues: 33.7181 Evaluate side-chains 138 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 134 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 156 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 16 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 30 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.163456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.117816 restraints weight = 8628.512| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.26 r_work: 0.3001 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 5830 Z= 0.106 Angle : 0.436 4.177 7946 Z= 0.229 Chirality : 0.034 0.129 978 Planarity : 0.003 0.024 974 Dihedral : 3.824 47.674 781 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.65 % Allowed : 13.92 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.08 (0.32), residues: 726 helix: 2.53 (0.21), residues: 613 sheet: None (None), residues: 0 loop : -0.86 (0.62), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 375 TYR 0.010 0.001 TYR A 359 PHE 0.008 0.001 PHE A 99 TRP 0.006 0.001 TRP B 324 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 5830) covalent geometry : angle 0.43558 ( 7946) hydrogen bonds : bond 0.03635 ( 465) hydrogen bonds : angle 3.49977 ( 1383) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 137 time to evaluate : 0.300 Fit side-chains REVERT: A 34 GLN cc_start: 0.8243 (tt0) cc_final: 0.7708 (tt0) REVERT: A 259 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7682 (mt-10) REVERT: A 284 ASN cc_start: 0.7438 (m-40) cc_final: 0.7206 (m-40) REVERT: A 339 ARG cc_start: 0.6908 (tpt170) cc_final: 0.6112 (mtp85) REVERT: A 451 MET cc_start: 0.7675 (mmt) cc_final: 0.6949 (ttt) REVERT: B 34 GLN cc_start: 0.8244 (tt0) cc_final: 0.7872 (tt0) REVERT: B 259 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7684 (mt-10) REVERT: B 339 ARG cc_start: 0.6789 (tpt170) cc_final: 0.6060 (mtp85) REVERT: B 451 MET cc_start: 0.7587 (mmt) cc_final: 0.6857 (ttt) outliers start: 4 outliers final: 2 residues processed: 138 average time/residue: 0.2089 time to fit residues: 36.0904 Evaluate side-chains 137 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 135 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 156 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 44 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 38 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.161431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.115612 restraints weight = 8598.456| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.27 r_work: 0.2992 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5830 Z= 0.130 Angle : 0.448 4.256 7946 Z= 0.237 Chirality : 0.035 0.135 978 Planarity : 0.003 0.026 974 Dihedral : 3.466 18.591 780 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.65 % Allowed : 14.89 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.22 (0.32), residues: 726 helix: 2.70 (0.21), residues: 601 sheet: None (None), residues: 0 loop : -0.88 (0.58), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 375 TYR 0.011 0.001 TYR B 359 PHE 0.010 0.001 PHE B 389 TRP 0.006 0.001 TRP A 324 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 5830) covalent geometry : angle 0.44844 ( 7946) hydrogen bonds : bond 0.03747 ( 465) hydrogen bonds : angle 3.52210 ( 1383) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 140 time to evaluate : 0.208 Fit side-chains REVERT: A 34 GLN cc_start: 0.8263 (tt0) cc_final: 0.7729 (tt0) REVERT: A 259 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7727 (mt-10) REVERT: A 339 ARG cc_start: 0.6941 (tpt170) cc_final: 0.6118 (mtp85) REVERT: A 451 MET cc_start: 0.7682 (mmt) cc_final: 0.6945 (ttt) REVERT: B 34 GLN cc_start: 0.8296 (tt0) cc_final: 0.7930 (tt0) REVERT: B 259 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7721 (mt-10) REVERT: B 339 ARG cc_start: 0.6842 (tpt170) cc_final: 0.6094 (mtp85) REVERT: B 451 MET cc_start: 0.7616 (mmt) cc_final: 0.6899 (ttt) outliers start: 4 outliers final: 2 residues processed: 140 average time/residue: 0.2105 time to fit residues: 36.2962 Evaluate side-chains 137 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 135 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 156 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 45 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.159981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.114198 restraints weight = 8566.113| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.26 r_work: 0.2961 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5830 Z= 0.148 Angle : 0.464 4.299 7946 Z= 0.246 Chirality : 0.035 0.132 978 Planarity : 0.003 0.027 974 Dihedral : 3.531 19.144 780 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.65 % Allowed : 15.05 % Favored : 84.30 % 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 are not related in a simple way. whole: 3.20 (0.32), residues: 726 helix: 2.67 (0.21), residues: 601 sheet: None (None), residues: 0 loop : -0.77 (0.58), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 463 TYR 0.011 0.002 TYR A 359 PHE 0.010 0.001 PHE A 351 TRP 0.007 0.002 TRP B 324 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 5830) covalent geometry : angle 0.46372 ( 7946) hydrogen bonds : bond 0.03843 ( 465) hydrogen bonds : angle 3.56719 ( 1383) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 142 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8322 (tt0) cc_final: 0.7801 (tt0) REVERT: A 259 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7757 (mt-10) REVERT: A 339 ARG cc_start: 0.6970 (tpt170) cc_final: 0.6126 (mtp85) REVERT: A 361 GLN cc_start: 0.7371 (mt0) cc_final: 0.7028 (mt0) REVERT: A 451 MET cc_start: 0.7740 (mmt) cc_final: 0.6976 (ttt) REVERT: B 34 GLN cc_start: 0.8328 (tt0) cc_final: 0.7967 (tt0) REVERT: B 156 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7770 (tt) REVERT: B 259 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7752 (mt-10) REVERT: B 339 ARG cc_start: 0.6865 (tpt170) cc_final: 0.6092 (mtp85) REVERT: B 451 MET cc_start: 0.7692 (mmt) cc_final: 0.6956 (ttt) outliers start: 4 outliers final: 1 residues processed: 143 average time/residue: 0.2178 time to fit residues: 38.7494 Evaluate side-chains 140 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 156 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 41 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.161156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.115780 restraints weight = 8513.416| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.26 r_work: 0.2978 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 5830 Z= 0.112 Angle : 0.444 4.196 7946 Z= 0.235 Chirality : 0.035 0.130 978 Planarity : 0.003 0.026 974 Dihedral : 3.481 18.736 780 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.49 % Allowed : 15.05 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.34 (0.32), residues: 726 helix: 2.73 (0.21), residues: 603 sheet: None (None), residues: 0 loop : -0.59 (0.61), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 375 TYR 0.010 0.001 TYR B 359 PHE 0.009 0.001 PHE B 99 TRP 0.006 0.001 TRP B 394 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 5830) covalent geometry : angle 0.44392 ( 7946) hydrogen bonds : bond 0.03651 ( 465) hydrogen bonds : angle 3.51441 ( 1383) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 147 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8255 (tt0) cc_final: 0.7718 (tt0) REVERT: A 259 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7721 (mt-10) REVERT: A 339 ARG cc_start: 0.6929 (tpt170) cc_final: 0.6095 (mtp85) REVERT: A 451 MET cc_start: 0.7723 (mmt) cc_final: 0.6969 (ttt) REVERT: B 34 GLN cc_start: 0.8308 (tt0) cc_final: 0.7942 (tt0) REVERT: B 156 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7768 (tt) REVERT: B 259 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7717 (mt-10) REVERT: B 339 ARG cc_start: 0.6821 (tpt170) cc_final: 0.6051 (mtp85) REVERT: B 451 MET cc_start: 0.7655 (mmt) cc_final: 0.6931 (ttt) outliers start: 3 outliers final: 2 residues processed: 148 average time/residue: 0.2030 time to fit residues: 37.7740 Evaluate side-chains 148 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 145 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 156 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 29 optimal weight: 0.4980 chunk 52 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 68 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.161195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.115671 restraints weight = 8684.220| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.27 r_work: 0.3001 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5830 Z= 0.114 Angle : 0.445 4.212 7946 Z= 0.234 Chirality : 0.035 0.129 978 Planarity : 0.003 0.027 974 Dihedral : 3.459 18.453 780 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.49 % Allowed : 15.37 % Favored : 84.14 % 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 are not related in a simple way. whole: 3.42 (0.32), residues: 726 helix: 2.77 (0.21), residues: 605 sheet: None (None), residues: 0 loop : -0.54 (0.61), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 463 TYR 0.010 0.001 TYR A 359 PHE 0.009 0.001 PHE A 99 TRP 0.006 0.001 TRP A 394 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 5830) covalent geometry : angle 0.44537 ( 7946) hydrogen bonds : bond 0.03589 ( 465) hydrogen bonds : angle 3.48483 ( 1383) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 149 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8279 (tt0) cc_final: 0.7749 (tt0) REVERT: A 259 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7757 (mt-10) REVERT: A 339 ARG cc_start: 0.6976 (tpt170) cc_final: 0.6145 (mtp85) REVERT: A 451 MET cc_start: 0.7736 (mmt) cc_final: 0.6972 (ttt) REVERT: B 34 GLN cc_start: 0.8334 (tt0) cc_final: 0.7968 (tt0) REVERT: B 156 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7805 (tt) REVERT: B 259 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7763 (mt-10) REVERT: B 339 ARG cc_start: 0.6873 (tpt170) cc_final: 0.6108 (mtp85) REVERT: B 451 MET cc_start: 0.7654 (mmt) cc_final: 0.6940 (ttt) outliers start: 3 outliers final: 1 residues processed: 150 average time/residue: 0.2061 time to fit residues: 38.4342 Evaluate side-chains 147 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 156 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 47 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.160586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.115193 restraints weight = 8704.545| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.28 r_work: 0.3000 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5830 Z= 0.106 Angle : 0.436 4.190 7946 Z= 0.231 Chirality : 0.035 0.128 978 Planarity : 0.003 0.027 974 Dihedral : 3.420 18.338 780 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.65 % Allowed : 15.70 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.49 (0.32), residues: 726 helix: 2.82 (0.21), residues: 605 sheet: None (None), residues: 0 loop : -0.51 (0.61), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 463 TYR 0.010 0.001 TYR A 359 PHE 0.009 0.001 PHE A 99 TRP 0.006 0.001 TRP A 394 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 5830) covalent geometry : angle 0.43604 ( 7946) hydrogen bonds : bond 0.03539 ( 465) hydrogen bonds : angle 3.45613 ( 1383) =============================================================================== Job complete usr+sys time: 2973.64 seconds wall clock time: 51 minutes 4.49 seconds (3064.49 seconds total)