Starting phenix.real_space_refine on Thu Mar 6 04:10:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7woc_32648/03_2025/7woc_32648.cif Found real_map, /net/cci-nas-00/data/ceres_data/7woc_32648/03_2025/7woc_32648.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7woc_32648/03_2025/7woc_32648.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7woc_32648/03_2025/7woc_32648.map" model { file = "/net/cci-nas-00/data/ceres_data/7woc_32648/03_2025/7woc_32648.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7woc_32648/03_2025/7woc_32648.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 3012 2.51 5 N 804 2.21 5 O 912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4746 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "A" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1560 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 12, 'TRANS': 191} Chain breaks: 2 Chain: "B" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1636 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 199} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.32, per 1000 atoms: 0.91 Number of scatterers: 4746 At special positions: 0 Unit cell: (91.02, 68.06, 119.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 912 8.00 N 804 7.00 C 3012 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 203 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 195 " distance=2.03 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 Links applied NAG-ASN " NAG C 601 " - " ASN C 343 " Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 592.7 milliseconds 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1132 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 14 sheets defined 6.1% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.904A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.612A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 386 through 390' Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.836A pdb=" N ASP A 90 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 91' Processing helix chain 'B' and resid 122 through 127 removed outlier: 3.749A pdb=" N LYS B 127 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 190 removed outlier: 3.766A pdb=" N LYS B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N HIS B 190 " --> pdb=" O ASP B 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 185 through 190' Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.543A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.663A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.724A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 5 through 6 removed outlier: 3.568A pdb=" N VAL A 20 " --> pdb=" O MET A 81 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 57 through 60 removed outlier: 3.604A pdb=" N ILE A 57 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 92 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 116 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 127 through 129 removed outlier: 3.835A pdb=" N LEU A 148 " --> pdb=" O PHE A 129 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 145 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 185 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL A 188 " --> pdb=" O HIS A 171 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N HIS A 171 " --> pdb=" O VAL A 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 157 through 159 removed outlier: 3.722A pdb=" N LYS A 216 " --> pdb=" O CYS A 203 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 5 through 6 removed outlier: 4.340A pdb=" N THR B 5 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG B 24 " --> pdb=" O THR B 5 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 12 through 13 Processing sheet with id=AB2, first strand: chain 'B' and resid 54 through 55 removed outlier: 6.726A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N TYR B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU B 34 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR B 98 " --> pdb=" O GLN B 91 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AB4, first strand: chain 'B' and resid 117 through 119 removed outlier: 3.742A pdb=" N PHE B 117 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 136 " --> pdb=" O PHE B 117 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 134 " --> pdb=" O PHE B 119 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ASN B 138 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU B 176 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 147 through 149 88 hydrogen bonds defined for protein. 228 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: 1.30 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1519 1.34 - 1.46: 1179 1.46 - 1.58: 2147 1.58 - 1.70: 0 1.70 - 1.81: 20 Bond restraints: 4865 Sorted by residual: bond pdb=" C PHE A 153 " pdb=" N PRO A 154 " ideal model delta sigma weight residual 1.331 1.357 -0.026 1.20e-02 6.94e+03 4.78e+00 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.85e+00 bond pdb=" C5 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.22e+00 bond pdb=" C GLU A 155 " pdb=" N PRO A 156 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.04e+00 bond pdb=" C3 NAG C 601 " pdb=" O3 NAG C 601 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 1.02e+00 ... (remaining 4860 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 6425 1.10 - 2.21: 131 2.21 - 3.31: 42 3.31 - 4.42: 10 4.42 - 5.52: 9 Bond angle restraints: 6617 Sorted by residual: angle pdb=" C VAL B 151 " pdb=" N ASP B 152 " pdb=" CA ASP B 152 " ideal model delta sigma weight residual 121.54 126.42 -4.88 1.91e+00 2.74e-01 6.52e+00 angle pdb=" C PRO A 154 " pdb=" N GLU A 155 " pdb=" CA GLU A 155 " ideal model delta sigma weight residual 120.26 123.62 -3.36 1.34e+00 5.57e-01 6.28e+00 angle pdb=" N ASP B 152 " pdb=" CA ASP B 152 " pdb=" C ASP B 152 " ideal model delta sigma weight residual 110.80 115.23 -4.43 2.13e+00 2.20e-01 4.32e+00 angle pdb=" N GLY B 69 " pdb=" CA GLY B 69 " pdb=" C GLY B 69 " ideal model delta sigma weight residual 113.18 117.74 -4.56 2.37e+00 1.78e-01 3.70e+00 angle pdb=" CA LYS A 208 " pdb=" C LYS A 208 " pdb=" N PRO A 209 " ideal model delta sigma weight residual 118.44 121.34 -2.90 1.59e+00 3.96e-01 3.33e+00 ... (remaining 6612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 2783 17.48 - 34.96: 101 34.96 - 52.44: 15 52.44 - 69.91: 9 69.91 - 87.39: 3 Dihedral angle restraints: 2911 sinusoidal: 1142 harmonic: 1769 Sorted by residual: dihedral pdb=" CA VAL B 151 " pdb=" C VAL B 151 " pdb=" N ASP B 152 " pdb=" CA ASP B 152 " ideal model delta harmonic sigma weight residual 180.00 160.20 19.80 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA CYS C 379 " pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " ideal model delta sinusoidal sigma weight residual 79.00 11.66 67.34 1 2.00e+01 2.50e-03 1.48e+01 dihedral pdb=" SG CYS C 391 " pdb=" CB CYS C 525 " pdb=" SG CYS C 525 " pdb=" CA CYS C 525 " ideal model delta sinusoidal sigma weight residual -73.00 -16.98 -56.02 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 2908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 400 0.025 - 0.050: 198 0.050 - 0.076: 58 0.076 - 0.101: 54 0.101 - 0.126: 19 Chirality restraints: 729 Sorted by residual: chirality pdb=" CA ILE B 59 " pdb=" N ILE B 59 " pdb=" C ILE B 59 " pdb=" CB ILE B 59 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA VAL A 157 " pdb=" N VAL A 157 " pdb=" C VAL A 157 " pdb=" CB VAL A 157 " 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 ILE C 434 " pdb=" N ILE C 434 " pdb=" C ILE C 434 " pdb=" CB ILE C 434 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.36e-01 ... (remaining 726 not shown) Planarity restraints: 856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO C 521 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 40 " 0.030 5.00e-02 4.00e+02 4.65e-02 3.45e+00 pdb=" N PRO A 41 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 41 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 41 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 14 " 0.019 5.00e-02 4.00e+02 2.94e-02 1.38e+00 pdb=" N PRO B 15 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 15 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 15 " 0.016 5.00e-02 4.00e+02 ... (remaining 853 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1314 2.81 - 3.33: 4052 3.33 - 3.86: 7727 3.86 - 4.38: 8853 4.38 - 4.90: 15570 Nonbonded interactions: 37516 Sorted by model distance: nonbonded pdb=" O GLU B 124 " pdb=" OG SER B 128 " model vdw 2.288 3.040 nonbonded pdb=" OG1 THR A 69 " pdb=" OE1 GLU A 82 " model vdw 2.320 3.040 nonbonded pdb=" OD1 ASN A 206 " pdb=" NZ LYS A 213 " model vdw 2.342 3.120 nonbonded pdb=" OD1 ASN C 448 " pdb=" ND2 ASN C 450 " model vdw 2.348 3.120 nonbonded pdb=" OD2 ASP C 398 " pdb=" OH TYR C 423 " model vdw 2.352 3.040 ... (remaining 37511 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.490 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.820 Find NCS groups from input model: 0.100 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:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 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 : 0.002 0.041 4865 Z= 0.122 Angle : 0.477 5.523 6617 Z= 0.256 Chirality : 0.041 0.126 729 Planarity : 0.004 0.047 855 Dihedral : 9.585 87.392 1755 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 4.60 % Allowed : 6.51 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.80 (0.27), residues: 600 helix: -4.88 (0.19), residues: 36 sheet: -2.38 (0.36), residues: 175 loop : -3.63 (0.24), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 353 HIS 0.001 0.000 HIS B 33 PHE 0.005 0.001 PHE B 140 TYR 0.005 0.001 TYR B 92 ARG 0.002 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 455 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7407 (tt) REVERT: A 122 SER cc_start: 0.8289 (m) cc_final: 0.7911 (p) REVERT: B 119 PHE cc_start: 0.5808 (m-80) cc_final: 0.5002 (m-80) REVERT: B 150 LYS cc_start: 0.5451 (mttp) cc_final: 0.5202 (tptp) REVERT: B 174 TYR cc_start: 0.7071 (m-80) cc_final: 0.6470 (m-80) outliers start: 24 outliers final: 7 residues processed: 189 average time/residue: 0.2151 time to fit residues: 48.5912 Evaluate side-chains 108 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 206 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 0.0970 chunk 18 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 439 ASN C 493 GLN A 1 GLN A 178 GLN B 30 ASN B 125 GLN B 148 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.156114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.124509 restraints weight = 7452.630| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.94 r_work: 0.3472 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 4865 Z= 0.206 Angle : 0.625 9.550 6617 Z= 0.312 Chirality : 0.044 0.173 729 Planarity : 0.005 0.048 855 Dihedral : 6.195 83.169 696 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 4.98 % Allowed : 14.37 % Favored : 80.65 % 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: -4.10 (0.30), residues: 600 helix: -4.74 (0.36), residues: 26 sheet: -2.22 (0.33), residues: 217 loop : -2.99 (0.28), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 36 HIS 0.005 0.001 HIS A 171 PHE 0.019 0.002 PHE B 47 TYR 0.013 0.002 TYR B 92 ARG 0.006 0.001 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 455 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7847 (tt) REVERT: A 27 ASP cc_start: 0.7837 (p0) cc_final: 0.7633 (p0) REVERT: A 122 SER cc_start: 0.8665 (m) cc_final: 0.8229 (p) REVERT: A 171 HIS cc_start: 0.7384 (m170) cc_final: 0.6773 (m170) REVERT: A 214 VAL cc_start: 0.7408 (OUTLIER) cc_final: 0.7133 (p) REVERT: B 150 LYS cc_start: 0.5453 (mttp) cc_final: 0.4990 (tptp) outliers start: 26 outliers final: 20 residues processed: 120 average time/residue: 0.1942 time to fit residues: 28.6803 Evaluate side-chains 108 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 206 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 0.0970 chunk 42 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 ASN B 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.149777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.118328 restraints weight = 7487.695| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.90 r_work: 0.3414 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 4865 Z= 0.230 Angle : 0.606 7.266 6617 Z= 0.304 Chirality : 0.044 0.151 729 Planarity : 0.005 0.045 855 Dihedral : 6.265 79.784 696 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 6.32 % Allowed : 15.13 % Favored : 78.54 % 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: -3.64 (0.31), residues: 600 helix: -4.20 (0.57), residues: 32 sheet: -1.70 (0.36), residues: 203 loop : -2.79 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.004 0.001 HIS A 207 PHE 0.020 0.002 PHE B 140 TYR 0.013 0.002 TYR A 152 ARG 0.003 0.001 ARG B 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 92 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: C 455 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.7963 (tt) REVERT: C 456 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.7942 (p90) REVERT: A 13 ARG cc_start: 0.8164 (mmm160) cc_final: 0.7743 (mmp-170) REVERT: A 171 HIS cc_start: 0.7593 (m170) cc_final: 0.7080 (m170) REVERT: B 82 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8106 (pp20) REVERT: B 83 ASP cc_start: 0.8667 (m-30) cc_final: 0.8312 (m-30) REVERT: B 143 ARG cc_start: 0.7067 (tmt-80) cc_final: 0.6852 (tmt-80) REVERT: B 150 LYS cc_start: 0.5578 (mttp) cc_final: 0.5088 (tptp) outliers start: 33 outliers final: 24 residues processed: 115 average time/residue: 0.2075 time to fit residues: 29.3312 Evaluate side-chains 107 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 206 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 22 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 0.3980 chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 ASN B 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.147380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.117034 restraints weight = 7510.373| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 3.30 r_work: 0.3374 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 4865 Z= 0.233 Angle : 0.592 7.013 6617 Z= 0.298 Chirality : 0.045 0.147 729 Planarity : 0.005 0.042 855 Dihedral : 6.349 78.435 696 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 5.94 % Allowed : 16.28 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.58 (0.32), residues: 600 helix: -4.02 (0.68), residues: 32 sheet: -1.73 (0.35), residues: 223 loop : -2.74 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.002 0.001 HIS A 207 PHE 0.018 0.002 PHE B 47 TYR 0.013 0.002 TYR B 92 ARG 0.006 0.001 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 408 ARG cc_start: 0.8555 (tmm160) cc_final: 0.8340 (ttp80) REVERT: C 455 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.7969 (tt) REVERT: C 456 PHE cc_start: 0.8736 (OUTLIER) cc_final: 0.8010 (p90) REVERT: A 13 ARG cc_start: 0.8175 (mmm160) cc_final: 0.7767 (mmp-170) REVERT: A 158 THR cc_start: 0.7375 (m) cc_final: 0.6913 (p) REVERT: A 171 HIS cc_start: 0.7750 (m170) cc_final: 0.7187 (m-70) REVERT: B 43 GLN cc_start: 0.8160 (pt0) cc_final: 0.7928 (pt0) REVERT: B 82 GLU cc_start: 0.8424 (tm-30) cc_final: 0.7952 (pp20) REVERT: B 83 ASP cc_start: 0.8634 (m-30) cc_final: 0.7971 (m-30) REVERT: B 149 TRP cc_start: 0.4879 (m100) cc_final: 0.4578 (m100) REVERT: B 150 LYS cc_start: 0.5960 (mttp) cc_final: 0.5381 (tptp) outliers start: 31 outliers final: 21 residues processed: 107 average time/residue: 0.1829 time to fit residues: 24.8239 Evaluate side-chains 107 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 206 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.145112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.114078 restraints weight = 7687.348| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 3.30 r_work: 0.3334 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 4865 Z= 0.259 Angle : 0.611 7.666 6617 Z= 0.308 Chirality : 0.045 0.153 729 Planarity : 0.005 0.043 855 Dihedral : 6.411 73.236 696 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 5.75 % Allowed : 17.05 % Favored : 77.20 % 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: -3.50 (0.33), residues: 600 helix: -3.91 (0.55), residues: 38 sheet: -1.68 (0.35), residues: 223 loop : -2.64 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 149 HIS 0.006 0.001 HIS A 207 PHE 0.019 0.002 PHE B 47 TYR 0.015 0.002 TYR A 32 ARG 0.005 0.000 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 408 ARG cc_start: 0.8637 (tmm160) cc_final: 0.8365 (ttp80) REVERT: C 455 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8068 (tt) REVERT: C 456 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8050 (p90) REVERT: A 158 THR cc_start: 0.7381 (m) cc_final: 0.6896 (p) REVERT: A 171 HIS cc_start: 0.7937 (m170) cc_final: 0.7424 (m-70) REVERT: B 82 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7863 (pp20) REVERT: B 83 ASP cc_start: 0.8665 (m-30) cc_final: 0.7898 (m-30) REVERT: B 149 TRP cc_start: 0.4811 (m100) cc_final: 0.4529 (m100) REVERT: B 150 LYS cc_start: 0.6226 (mttp) cc_final: 0.5576 (tptp) outliers start: 30 outliers final: 22 residues processed: 101 average time/residue: 0.1893 time to fit residues: 24.0694 Evaluate side-chains 100 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 166 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 51 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.140215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.108255 restraints weight = 7903.595| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.98 r_work: 0.3267 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.5544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 4865 Z= 0.461 Angle : 0.723 8.843 6617 Z= 0.372 Chirality : 0.050 0.184 729 Planarity : 0.005 0.042 855 Dihedral : 6.871 72.325 694 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 6.32 % Allowed : 18.39 % Favored : 75.29 % 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: -3.66 (0.32), residues: 600 helix: -4.07 (0.47), residues: 44 sheet: -1.73 (0.38), residues: 197 loop : -2.72 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 149 HIS 0.008 0.002 HIS A 207 PHE 0.028 0.003 PHE C 429 TYR 0.019 0.003 TYR A 152 ARG 0.004 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 76 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 455 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8140 (tt) REVERT: C 456 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8291 (p90) REVERT: A 10 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7297 (mt-10) REVERT: A 13 ARG cc_start: 0.8047 (mmm160) cc_final: 0.7658 (mmp-170) REVERT: B 82 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7945 (pp20) REVERT: B 149 TRP cc_start: 0.5018 (m100) cc_final: 0.4642 (m100) REVERT: B 150 LYS cc_start: 0.6763 (mttp) cc_final: 0.5833 (tptp) outliers start: 33 outliers final: 28 residues processed: 98 average time/residue: 0.2799 time to fit residues: 35.4033 Evaluate side-chains 105 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 74 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 166 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 44 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 31 optimal weight: 0.1980 chunk 53 optimal weight: 0.0170 chunk 39 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 0.3980 chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 overall best weight: 0.3618 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.145258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.114440 restraints weight = 7618.212| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 3.15 r_work: 0.3351 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4865 Z= 0.173 Angle : 0.598 8.134 6617 Z= 0.300 Chirality : 0.045 0.164 729 Planarity : 0.004 0.040 855 Dihedral : 6.194 69.492 694 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 4.21 % Allowed : 20.88 % Favored : 74.90 % 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: -3.34 (0.33), residues: 600 helix: -3.99 (0.48), residues: 44 sheet: -1.56 (0.36), residues: 217 loop : -2.46 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.004 0.001 HIS A 207 PHE 0.013 0.001 PHE B 47 TYR 0.014 0.001 TYR A 105 ARG 0.004 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 455 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.7947 (tt) REVERT: C 456 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.7921 (p90) REVERT: A 10 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7195 (mt-10) REVERT: A 158 THR cc_start: 0.7714 (m) cc_final: 0.7225 (p) REVERT: B 83 ASP cc_start: 0.8620 (m-30) cc_final: 0.8307 (m-30) REVERT: B 119 PHE cc_start: 0.6247 (m-10) cc_final: 0.5986 (m-80) REVERT: B 149 TRP cc_start: 0.4950 (m100) cc_final: 0.4654 (m100) REVERT: B 150 LYS cc_start: 0.6860 (mttp) cc_final: 0.6090 (tptp) outliers start: 22 outliers final: 18 residues processed: 92 average time/residue: 0.2378 time to fit residues: 29.1135 Evaluate side-chains 96 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 166 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 20 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 0.0070 chunk 23 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.142955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.111809 restraints weight = 7661.598| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.78 r_work: 0.3324 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.5441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4865 Z= 0.245 Angle : 0.633 8.406 6617 Z= 0.319 Chirality : 0.046 0.149 729 Planarity : 0.004 0.040 855 Dihedral : 6.112 68.713 694 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.50 % Favored : 88.50 % Rotamer: Outliers : 4.79 % Allowed : 21.46 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.21 (0.33), residues: 600 helix: -3.96 (0.47), residues: 44 sheet: -1.49 (0.36), residues: 214 loop : -2.35 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.005 0.001 HIS A 207 PHE 0.016 0.002 PHE B 47 TYR 0.014 0.002 TYR A 105 ARG 0.005 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 455 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8004 (tt) REVERT: C 456 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.7992 (p90) REVERT: A 10 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7218 (mt-10) REVERT: A 158 THR cc_start: 0.7528 (m) cc_final: 0.6963 (p) REVERT: B 83 ASP cc_start: 0.8608 (m-30) cc_final: 0.8354 (m-30) REVERT: B 119 PHE cc_start: 0.6211 (m-10) cc_final: 0.5986 (m-80) REVERT: B 149 TRP cc_start: 0.4949 (m100) cc_final: 0.4604 (m100) REVERT: B 150 LYS cc_start: 0.7012 (mttp) cc_final: 0.6106 (tptp) outliers start: 25 outliers final: 21 residues processed: 94 average time/residue: 0.2442 time to fit residues: 28.6194 Evaluate side-chains 98 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 166 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 0.0770 chunk 52 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.140202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.109237 restraints weight = 7748.025| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.82 r_work: 0.3280 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.5794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 4865 Z= 0.435 Angle : 0.732 9.451 6617 Z= 0.374 Chirality : 0.050 0.172 729 Planarity : 0.005 0.049 855 Dihedral : 6.358 66.304 693 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.50 % Favored : 86.50 % Rotamer: Outliers : 4.98 % Allowed : 21.26 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.36 (0.32), residues: 600 helix: -3.86 (0.48), residues: 44 sheet: -1.47 (0.39), residues: 192 loop : -2.54 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 436 HIS 0.008 0.002 HIS A 207 PHE 0.027 0.002 PHE C 429 TYR 0.018 0.003 TYR A 105 ARG 0.006 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: C 455 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8114 (tt) REVERT: C 456 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8366 (p90) REVERT: A 10 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7380 (mt-10) REVERT: A 13 ARG cc_start: 0.7983 (mmm160) cc_final: 0.7657 (mmp-170) REVERT: A 178 GLN cc_start: 0.5920 (mt0) cc_final: 0.5407 (mm-40) REVERT: B 83 ASP cc_start: 0.8722 (m-30) cc_final: 0.8454 (m-30) REVERT: B 149 TRP cc_start: 0.5028 (m100) cc_final: 0.4629 (m100) REVERT: B 150 LYS cc_start: 0.6937 (mttp) cc_final: 0.5987 (tptp) outliers start: 26 outliers final: 24 residues processed: 92 average time/residue: 0.1818 time to fit residues: 21.0467 Evaluate side-chains 97 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 166 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.0060 chunk 54 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 10 optimal weight: 0.2980 chunk 22 optimal weight: 0.9980 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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 = 0.3967 r_free = 0.3967 target = 0.144580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.113965 restraints weight = 7686.612| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 3.23 r_work: 0.3335 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.5652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4865 Z= 0.200 Angle : 0.626 8.615 6617 Z= 0.315 Chirality : 0.046 0.147 729 Planarity : 0.004 0.040 855 Dihedral : 5.857 62.099 692 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 3.83 % Allowed : 22.80 % Favored : 73.37 % 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: -3.10 (0.33), residues: 600 helix: -3.72 (0.54), residues: 44 sheet: -1.46 (0.40), residues: 188 loop : -2.24 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.005 0.001 HIS A 207 PHE 0.013 0.001 PHE B 47 TYR 0.015 0.001 TYR A 105 ARG 0.004 0.000 ARG B 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 455 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.7945 (tt) REVERT: C 456 PHE cc_start: 0.8664 (OUTLIER) cc_final: 0.7940 (p90) REVERT: A 10 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7470 (mt-10) REVERT: A 158 THR cc_start: 0.7860 (m) cc_final: 0.7632 (t) REVERT: A 171 HIS cc_start: 0.7814 (m90) cc_final: 0.7381 (m-70) REVERT: B 83 ASP cc_start: 0.8629 (m-30) cc_final: 0.8354 (m-30) REVERT: B 149 TRP cc_start: 0.4967 (m100) cc_final: 0.4598 (m100) REVERT: B 150 LYS cc_start: 0.7007 (mttp) cc_final: 0.6094 (tptp) outliers start: 20 outliers final: 17 residues processed: 95 average time/residue: 0.1546 time to fit residues: 19.1974 Evaluate side-chains 98 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 166 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 39 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 28 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.143838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.113205 restraints weight = 7705.988| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 3.17 r_work: 0.3322 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.5682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4865 Z= 0.227 Angle : 0.636 8.830 6617 Z= 0.320 Chirality : 0.046 0.145 729 Planarity : 0.004 0.039 855 Dihedral : 5.818 63.079 692 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 4.60 % Allowed : 22.80 % Favored : 72.61 % 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: -3.03 (0.34), residues: 600 helix: -3.71 (0.55), residues: 44 sheet: -1.30 (0.39), residues: 195 loop : -2.26 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.006 0.001 HIS A 207 PHE 0.015 0.002 PHE B 47 TYR 0.016 0.002 TYR A 105 ARG 0.003 0.000 ARG B 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3688.12 seconds wall clock time: 64 minutes 52.09 seconds (3892.09 seconds total)