Starting phenix.real_space_refine on Tue Jul 29 19:17:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wcb_21605/07_2025/6wcb_21605.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wcb_21605/07_2025/6wcb_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_21605/07_2025/6wcb_21605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wcb_21605/07_2025/6wcb_21605.map" model { file = "/net/cci-nas-00/data/ceres_data/6wcb_21605/07_2025/6wcb_21605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wcb_21605/07_2025/6wcb_21605.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.61, per 1000 atoms: 0.57 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: 3.27 Conformation dependent library (CDL) restraints added in 909.0 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: 0.76 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: 4.14 Time building geometry restraints manager: 3.86 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 508 or resid 701 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: 0.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.210 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 28.980 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 33.260 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.005 0.001 TRP A 394 HIS 0.003 0.001 HIS A 328 PHE 0.025 0.001 PHE A 420 TYR 0.004 0.001 TYR B 313 ARG 0.001 0.000 ARG A 370 Details of bonding type rmsd hydrogen bonds : bond 0.11405 ( 465) hydrogen bonds : angle 4.57285 ( 1383) covalent geometry : bond 0.00454 ( 5830) covalent geometry : angle 0.41400 ( 7946) *********************** 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 : 0.761 Fit side-chains 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: 0.5835 (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: 0.7521 (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: 0.7168 (ttt) outliers start: 8 outliers final: 4 residues processed: 139 average time/residue: 0.3733 time to fit residues: 68.4450 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 : 0.906 ------------------------------------------------------------------------------- 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 60 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.168325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.124072 restraints weight = 7560.880| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.17 r_work: 0.3107 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5830 Z= 0.158 Angle : 0.484 5.122 7946 Z= 0.254 Chirality : 0.035 0.126 978 Planarity : 0.004 0.037 974 Dihedral : 4.996 53.421 784 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 1.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.46 % Allowed : 10.03 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.32), residues: 726 helix: 1.90 (0.21), residues: 597 sheet: None (None), residues: 0 loop : -2.03 (0.53), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 324 HIS 0.007 0.001 HIS A 328 PHE 0.010 0.001 PHE A 295 TYR 0.011 0.002 TYR A 359 ARG 0.002 0.000 ARG A 260 Details of bonding type rmsd hydrogen bonds : bond 0.04221 ( 465) hydrogen bonds : angle 3.83278 ( 1383) covalent geometry : bond 0.00351 ( 5830) covalent geometry : angle 0.48442 ( 7946) *********************** 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 130 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8251 (tt0) cc_final: 0.7758 (tt0) REVERT: A 131 VAL cc_start: 0.8280 (OUTLIER) cc_final: 0.8039 (t) REVERT: A 339 ARG cc_start: 0.6864 (tpt170) cc_final: 0.6072 (mtp85) REVERT: A 362 THR cc_start: 0.8210 (m) cc_final: 0.7974 (p) REVERT: A 451 MET cc_start: 0.7716 (mmt) cc_final: 0.6927 (ttt) REVERT: B 34 GLN cc_start: 0.8270 (tt0) cc_final: 0.7895 (tt0) REVERT: B 131 VAL cc_start: 0.8209 (OUTLIER) cc_final: 0.7939 (t) REVERT: B 259 GLU cc_start: 0.7964 (mp0) cc_final: 0.7737 (mp0) REVERT: B 339 ARG cc_start: 0.6801 (tpt170) cc_final: 0.6055 (mtp85) REVERT: B 362 THR cc_start: 0.8157 (m) cc_final: 0.7956 (p) REVERT: B 451 MET cc_start: 0.7723 (mmt) cc_final: 0.6954 (ttt) outliers start: 9 outliers final: 7 residues processed: 126 average time/residue: 0.4758 time to fit residues: 74.6569 Evaluate side-chains 130 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 17 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 64 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.165002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.119073 restraints weight = 8530.285| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.28 r_work: 0.3047 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5830 Z= 0.139 Angle : 0.459 4.257 7946 Z= 0.243 Chirality : 0.035 0.158 978 Planarity : 0.003 0.023 974 Dihedral : 4.861 51.214 784 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.94 % Allowed : 11.81 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.32), residues: 726 helix: 2.27 (0.21), residues: 597 sheet: None (None), residues: 0 loop : -1.48 (0.55), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 394 HIS 0.006 0.001 HIS A 328 PHE 0.009 0.001 PHE A 389 TYR 0.009 0.001 TYR B 359 ARG 0.004 0.000 ARG A 375 Details of bonding type rmsd hydrogen bonds : bond 0.04137 ( 465) hydrogen bonds : angle 3.73373 ( 1383) covalent geometry : bond 0.00306 ( 5830) covalent geometry : angle 0.45929 ( 7946) *********************** 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 144 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8260 (tt0) cc_final: 0.7718 (tt0) REVERT: A 131 VAL cc_start: 0.8298 (OUTLIER) cc_final: 0.8081 (t) REVERT: A 259 GLU cc_start: 0.7930 (mp0) cc_final: 0.7697 (mp0) REVERT: A 339 ARG cc_start: 0.6911 (tpt170) cc_final: 0.6110 (mtp85) REVERT: A 451 MET cc_start: 0.7659 (mmt) cc_final: 0.6882 (ttt) REVERT: B 34 GLN cc_start: 0.8320 (tt0) cc_final: 0.7936 (tt0) REVERT: B 131 VAL cc_start: 0.8295 (OUTLIER) cc_final: 0.8059 (t) REVERT: B 259 GLU cc_start: 0.8053 (mp0) cc_final: 0.7766 (mp0) REVERT: B 339 ARG cc_start: 0.6830 (tpt170) cc_final: 0.6101 (mtp85) REVERT: B 451 MET cc_start: 0.7700 (mmt) cc_final: 0.6897 (ttt) outliers start: 12 outliers final: 7 residues processed: 138 average time/residue: 0.4859 time to fit residues: 84.7628 Evaluate side-chains 136 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 431 LEU 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 Chi-restraints excluded: chain B residue 363 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 35 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.162214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.115844 restraints weight = 8748.485| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.30 r_work: 0.2986 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5830 Z= 0.147 Angle : 0.462 4.326 7946 Z= 0.245 Chirality : 0.035 0.121 978 Planarity : 0.004 0.024 974 Dihedral : 4.684 50.089 784 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.78 % Allowed : 11.49 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.32), residues: 726 helix: 2.46 (0.21), residues: 597 sheet: None (None), residues: 0 loop : -1.07 (0.57), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 324 HIS 0.005 0.001 HIS A 328 PHE 0.010 0.001 PHE A 351 TYR 0.010 0.002 TYR B 359 ARG 0.005 0.001 ARG A 375 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 465) hydrogen bonds : angle 3.63673 ( 1383) covalent geometry : bond 0.00327 ( 5830) covalent geometry : angle 0.46188 ( 7946) *********************** 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 148 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8249 (tt0) cc_final: 0.7711 (tt0) REVERT: A 131 VAL cc_start: 0.8264 (OUTLIER) cc_final: 0.8059 (t) REVERT: A 156 LEU cc_start: 0.8453 (mt) cc_final: 0.8241 (mt) REVERT: A 339 ARG cc_start: 0.6916 (tpt170) cc_final: 0.6113 (mtp85) REVERT: A 451 MET cc_start: 0.7678 (mmt) cc_final: 0.6886 (ttt) REVERT: B 34 GLN cc_start: 0.8286 (tt0) cc_final: 0.7888 (tt0) REVERT: B 131 VAL cc_start: 0.8304 (OUTLIER) cc_final: 0.8075 (t) REVERT: B 339 ARG cc_start: 0.6829 (tpt170) cc_final: 0.6102 (mtp85) REVERT: B 451 MET cc_start: 0.7648 (mmt) cc_final: 0.6863 (ttt) outliers start: 11 outliers final: 7 residues processed: 143 average time/residue: 0.4412 time to fit residues: 80.0616 Evaluate side-chains 142 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 431 LEU 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 Chi-restraints excluded: chain B residue 363 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 15 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.160658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.114768 restraints weight = 8556.812| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.25 r_work: 0.2972 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 5830 Z= 0.158 Angle : 0.473 4.338 7946 Z= 0.252 Chirality : 0.036 0.198 978 Planarity : 0.003 0.024 974 Dihedral : 4.527 48.841 784 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.29 % Allowed : 14.08 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.32), residues: 726 helix: 2.47 (0.21), residues: 599 sheet: None (None), residues: 0 loop : -0.97 (0.58), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 394 HIS 0.005 0.001 HIS A 328 PHE 0.010 0.001 PHE A 351 TYR 0.010 0.002 TYR B 359 ARG 0.002 0.000 ARG B 375 Details of bonding type rmsd hydrogen bonds : bond 0.04050 ( 465) hydrogen bonds : angle 3.66131 ( 1383) covalent geometry : bond 0.00355 ( 5830) covalent geometry : angle 0.47335 ( 7946) *********************** 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 141 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8278 (tt0) cc_final: 0.7728 (tt0) REVERT: A 259 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7688 (mt-10) REVERT: A 339 ARG cc_start: 0.6959 (tpt170) cc_final: 0.6129 (mtp85) REVERT: A 451 MET cc_start: 0.7707 (mmt) cc_final: 0.6949 (ttt) REVERT: B 34 GLN cc_start: 0.8331 (tt0) cc_final: 0.7965 (tt0) REVERT: B 339 ARG cc_start: 0.6856 (tpt170) cc_final: 0.6092 (mtp85) REVERT: B 451 MET cc_start: 0.7681 (mmt) cc_final: 0.6893 (ttt) outliers start: 8 outliers final: 3 residues processed: 136 average time/residue: 0.4631 time to fit residues: 79.1887 Evaluate side-chains 135 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 132 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 363 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 16 optimal weight: 0.3980 chunk 3 optimal weight: 0.0060 chunk 30 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.8398 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.163004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.117802 restraints weight = 8633.231| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.25 r_work: 0.3008 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 5830 Z= 0.092 Angle : 0.430 4.085 7946 Z= 0.226 Chirality : 0.034 0.125 978 Planarity : 0.003 0.026 974 Dihedral : 3.402 18.384 780 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.81 % Allowed : 14.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.13 (0.32), residues: 726 helix: 2.56 (0.21), residues: 613 sheet: None (None), residues: 0 loop : -0.84 (0.62), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 324 HIS 0.003 0.001 HIS A 328 PHE 0.007 0.001 PHE B 99 TYR 0.010 0.001 TYR A 359 ARG 0.003 0.000 ARG B 375 Details of bonding type rmsd hydrogen bonds : bond 0.03537 ( 465) hydrogen bonds : angle 3.52109 ( 1383) covalent geometry : bond 0.00184 ( 5830) covalent geometry : angle 0.42969 ( 7946) *********************** 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 142 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 137 time to evaluate : 0.801 Fit side-chains REVERT: A 34 GLN cc_start: 0.8241 (tt0) cc_final: 0.7700 (tt0) REVERT: A 259 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7677 (mt-10) REVERT: A 339 ARG cc_start: 0.6918 (tpt170) cc_final: 0.6110 (mtp85) REVERT: A 451 MET cc_start: 0.7661 (mmt) cc_final: 0.6952 (ttt) REVERT: B 34 GLN cc_start: 0.8253 (tt0) cc_final: 0.7875 (tt0) REVERT: B 156 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7690 (tt) REVERT: B 259 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7679 (mt-10) REVERT: B 339 ARG cc_start: 0.6820 (tpt170) cc_final: 0.6086 (mtp85) REVERT: B 451 MET cc_start: 0.7595 (mmt) cc_final: 0.6897 (ttt) outliers start: 5 outliers final: 2 residues processed: 137 average time/residue: 0.4312 time to fit residues: 75.6136 Evaluate side-chains 138 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 135 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 431 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 10 optimal weight: 8.9990 chunk 25 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 40.0000 chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.161313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.115379 restraints weight = 8686.056| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.27 r_work: 0.2990 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3119 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= 0.143 Angle : 0.456 4.299 7946 Z= 0.240 Chirality : 0.035 0.162 978 Planarity : 0.003 0.026 974 Dihedral : 3.470 18.820 780 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 1.98 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.20 (0.32), residues: 726 helix: 2.68 (0.21), residues: 601 sheet: None (None), residues: 0 loop : -0.88 (0.57), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 324 HIS 0.006 0.001 HIS A 328 PHE 0.011 0.001 PHE A 389 TYR 0.011 0.002 TYR A 359 ARG 0.004 0.000 ARG B 463 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 465) hydrogen bonds : angle 3.56222 ( 1383) covalent geometry : bond 0.00319 ( 5830) covalent geometry : angle 0.45551 ( 7946) *********************** 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 : 0.759 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8299 (tt0) cc_final: 0.7762 (tt0) REVERT: A 259 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7714 (mt-10) REVERT: A 339 ARG cc_start: 0.6961 (tpt170) cc_final: 0.6131 (mtp85) REVERT: A 451 MET cc_start: 0.7704 (mmt) cc_final: 0.6953 (ttt) REVERT: B 34 GLN cc_start: 0.8322 (tt0) cc_final: 0.7939 (tt0) REVERT: B 259 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7709 (mt-10) REVERT: B 339 ARG cc_start: 0.6864 (tpt170) cc_final: 0.6110 (mtp85) REVERT: B 451 MET cc_start: 0.7652 (mmt) cc_final: 0.6938 (ttt) outliers start: 4 outliers final: 3 residues processed: 140 average time/residue: 0.4201 time to fit residues: 75.9019 Evaluate side-chains 137 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 134 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 431 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 18 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.156985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.110079 restraints weight = 8594.301| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.32 r_work: 0.2928 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 5830 Z= 0.210 Angle : 0.502 4.481 7946 Z= 0.269 Chirality : 0.037 0.133 978 Planarity : 0.004 0.027 974 Dihedral : 3.653 19.688 780 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.97 % Allowed : 15.53 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.32), residues: 726 helix: 2.46 (0.21), residues: 601 sheet: None (None), residues: 0 loop : -0.76 (0.57), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 324 HIS 0.005 0.001 HIS A 328 PHE 0.012 0.002 PHE B 351 TYR 0.013 0.002 TYR B 359 ARG 0.003 0.000 ARG A 375 Details of bonding type rmsd hydrogen bonds : bond 0.04222 ( 465) hydrogen bonds : angle 3.68979 ( 1383) covalent geometry : bond 0.00483 ( 5830) covalent geometry : angle 0.50187 ( 7946) *********************** 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 149 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 143 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8389 (tt0) cc_final: 0.7877 (tt0) REVERT: A 339 ARG cc_start: 0.7038 (tpt170) cc_final: 0.6168 (mtp85) REVERT: A 451 MET cc_start: 0.7744 (mmt) cc_final: 0.6989 (ttt) REVERT: B 34 GLN cc_start: 0.8392 (tt0) cc_final: 0.8047 (tt0) REVERT: B 156 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7797 (tt) REVERT: B 339 ARG cc_start: 0.6929 (tpt170) cc_final: 0.6132 (mtp85) REVERT: B 451 MET cc_start: 0.7724 (mmt) cc_final: 0.6986 (ttt) outliers start: 6 outliers final: 2 residues processed: 144 average time/residue: 0.4195 time to fit residues: 77.7009 Evaluate side-chains 142 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 139 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 431 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 44 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.157750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.111823 restraints weight = 8633.261| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.28 r_work: 0.2936 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5830 Z= 0.163 Angle : 0.479 4.346 7946 Z= 0.255 Chirality : 0.036 0.130 978 Planarity : 0.003 0.027 974 Dihedral : 3.633 19.428 780 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.81 % Allowed : 16.34 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.32), residues: 726 helix: 2.45 (0.21), residues: 601 sheet: None (None), residues: 0 loop : -0.68 (0.58), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 324 HIS 0.006 0.001 HIS A 57 PHE 0.010 0.001 PHE A 389 TYR 0.010 0.002 TYR A 359 ARG 0.003 0.000 ARG A 375 Details of bonding type rmsd hydrogen bonds : bond 0.04044 ( 465) hydrogen bonds : angle 3.63913 ( 1383) covalent geometry : bond 0.00371 ( 5830) covalent geometry : angle 0.47930 ( 7946) *********************** 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 149 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 144 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8357 (tt0) cc_final: 0.7855 (tt0) REVERT: A 339 ARG cc_start: 0.7032 (tpt170) cc_final: 0.6154 (mtp85) REVERT: A 375 ARG cc_start: 0.7795 (mtm-85) cc_final: 0.7572 (mtm-85) REVERT: A 451 MET cc_start: 0.7752 (mmt) cc_final: 0.6984 (ttt) REVERT: B 34 GLN cc_start: 0.8370 (tt0) cc_final: 0.8013 (tt0) REVERT: B 156 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7852 (tt) REVERT: B 259 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7801 (mt-10) REVERT: B 339 ARG cc_start: 0.6911 (tpt170) cc_final: 0.6094 (mtp85) REVERT: B 451 MET cc_start: 0.7736 (mmt) cc_final: 0.6991 (ttt) outliers start: 5 outliers final: 2 residues processed: 145 average time/residue: 0.4534 time to fit residues: 83.8397 Evaluate side-chains 147 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 144 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 431 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 18 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.157824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.112252 restraints weight = 8908.071| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.28 r_work: 0.2952 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5830 Z= 0.162 Angle : 0.477 4.334 7946 Z= 0.255 Chirality : 0.036 0.130 978 Planarity : 0.003 0.027 974 Dihedral : 3.642 19.389 780 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.65 % Allowed : 16.83 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.32), residues: 726 helix: 2.48 (0.21), residues: 601 sheet: None (None), residues: 0 loop : -0.65 (0.58), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 324 HIS 0.006 0.001 HIS A 57 PHE 0.010 0.001 PHE B 389 TYR 0.011 0.002 TYR B 359 ARG 0.002 0.000 ARG B 260 Details of bonding type rmsd hydrogen bonds : bond 0.04010 ( 465) hydrogen bonds : angle 3.62164 ( 1383) covalent geometry : bond 0.00368 ( 5830) covalent geometry : angle 0.47743 ( 7946) ********************** 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: 4 poor density : 148 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8379 (tt0) cc_final: 0.7860 (tt0) REVERT: A 339 ARG cc_start: 0.7044 (tpt170) cc_final: 0.6170 (mtp85) REVERT: A 451 MET cc_start: 0.7756 (mmt) cc_final: 0.6983 (ttt) REVERT: B 34 GLN cc_start: 0.8358 (tt0) cc_final: 0.8002 (tt0) REVERT: B 156 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7766 (tt) REVERT: B 259 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7780 (mt-10) REVERT: B 339 ARG cc_start: 0.6926 (tpt170) cc_final: 0.6103 (mtp85) REVERT: B 451 MET cc_start: 0.7739 (mmt) cc_final: 0.6980 (ttt) outliers start: 4 outliers final: 2 residues processed: 149 average time/residue: 0.4477 time to fit residues: 85.2121 Evaluate side-chains 151 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 148 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 431 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 42 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 50 optimal weight: 0.0470 chunk 22 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.5084 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.159902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.114656 restraints weight = 9026.830| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.29 r_work: 0.2971 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5830 Z= 0.104 Angle : 0.454 4.148 7946 Z= 0.239 Chirality : 0.036 0.227 978 Planarity : 0.003 0.028 974 Dihedral : 3.538 18.663 780 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.65 % Allowed : 17.31 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.27 (0.32), residues: 726 helix: 2.65 (0.21), residues: 605 sheet: None (None), residues: 0 loop : -0.51 (0.60), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 394 HIS 0.005 0.001 HIS A 57 PHE 0.008 0.001 PHE B 99 TYR 0.010 0.001 TYR A 359 ARG 0.002 0.000 ARG B 463 Details of bonding type rmsd hydrogen bonds : bond 0.03654 ( 465) hydrogen bonds : angle 3.52335 ( 1383) covalent geometry : bond 0.00220 ( 5830) covalent geometry : angle 0.45381 ( 7946) =============================================================================== Job complete usr+sys time: 6136.28 seconds wall clock time: 104 minutes 40.33 seconds (6280.33 seconds total)