Starting phenix.real_space_refine on Fri Aug 22 20:55:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cpd_16779/08_2025/8cpd_16779.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cpd_16779/08_2025/8cpd_16779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cpd_16779/08_2025/8cpd_16779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cpd_16779/08_2025/8cpd_16779.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cpd_16779/08_2025/8cpd_16779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cpd_16779/08_2025/8cpd_16779.map" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 44 5.16 5 C 5096 2.51 5 N 1374 2.21 5 O 1514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8030 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2173 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 11, 'TRANS': 257} Chain breaks: 2 Chain: "C" Number of atoms: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1842 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 5, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2173 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 11, 'TRANS': 257} Chain breaks: 2 Chain: "D" Number of atoms: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1842 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 5, 'TRANS': 222} Chain breaks: 1 Time building chain proxies: 2.22, per 1000 atoms: 0.28 Number of scatterers: 8030 At special positions: 0 Unit cell: (85.527, 91.375, 97.954, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 2 15.00 O 1514 8.00 N 1374 7.00 C 5096 6.00 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: 0.70 Conformation dependent library (CDL) restraints added in 441.7 milliseconds Enol-peptide restraints added in 1.4 microseconds 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1908 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 4 sheets defined 62.5% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 383 through 398 Processing helix chain 'A' and resid 429 through 434 removed outlier: 3.607A pdb=" N HIS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 462 removed outlier: 4.156A pdb=" N ASP A 447 " --> pdb=" O PHE A 443 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE A 448 " --> pdb=" O GLN A 444 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ALA A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 519 Processing helix chain 'A' and resid 526 through 544 removed outlier: 4.151A pdb=" N ASP A 530 " --> pdb=" O SER A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 563 Processing helix chain 'A' and resid 578 through 589 removed outlier: 3.645A pdb=" N LYS A 582 " --> pdb=" O PRO A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 613 Processing helix chain 'C' and resid 5 through 19 Processing helix chain 'C' and resid 21 through 35 removed outlier: 3.841A pdb=" N MET C 25 " --> pdb=" O ARG C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 71 removed outlier: 3.981A pdb=" N LYS C 71 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 110 Processing helix chain 'C' and resid 111 through 115 Processing helix chain 'C' and resid 117 through 137 Processing helix chain 'C' and resid 141 through 165 Processing helix chain 'C' and resid 170 through 187 Processing helix chain 'C' and resid 190 through 208 removed outlier: 3.695A pdb=" N ALA C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 236 removed outlier: 4.210A pdb=" N LEU C 222 " --> pdb=" O LYS C 218 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE C 223 " --> pdb=" O ASP C 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 399 removed outlier: 3.777A pdb=" N LYS B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 434 removed outlier: 3.593A pdb=" N HIS B 434 " --> pdb=" O TYR B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 462 removed outlier: 4.139A pdb=" N ASP B 447 " --> pdb=" O PHE B 443 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE B 448 " --> pdb=" O GLN B 444 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALA B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 519 Processing helix chain 'B' and resid 526 through 544 removed outlier: 4.119A pdb=" N ASP B 530 " --> pdb=" O SER B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 563 Processing helix chain 'B' and resid 578 through 589 removed outlier: 3.518A pdb=" N LYS B 582 " --> pdb=" O PRO B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 613 Processing helix chain 'D' and resid 5 through 19 Processing helix chain 'D' and resid 21 through 36 removed outlier: 3.824A pdb=" N MET D 25 " --> pdb=" O ARG D 21 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLY D 36 " --> pdb=" O VAL D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 71 removed outlier: 3.996A pdb=" N LYS D 71 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 110 Processing helix chain 'D' and resid 117 through 137 Processing helix chain 'D' and resid 141 through 165 Processing helix chain 'D' and resid 170 through 187 Processing helix chain 'D' and resid 190 through 208 removed outlier: 3.678A pdb=" N ALA D 194 " --> pdb=" O SER D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 236 removed outlier: 4.210A pdb=" N LEU D 222 " --> pdb=" O LYS D 218 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE D 223 " --> pdb=" O ASP D 219 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 350 through 353 removed outlier: 5.525A pdb=" N LEU A 351 " --> pdb=" O LYS A 367 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LYS A 367 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 419 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLN A 422 " --> pdb=" O PHE A 408 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N PHE A 408 " --> pdb=" O GLN A 422 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 474 through 477 Processing sheet with id=AA3, first strand: chain 'B' and resid 350 through 353 removed outlier: 5.530A pdb=" N LEU B 351 " --> pdb=" O LYS B 367 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LYS B 367 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE B 419 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLN B 422 " --> pdb=" O PHE B 408 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N PHE B 408 " --> pdb=" O GLN B 422 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 474 through 477 492 hydrogen bonds defined for protein. 1458 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: 1.13 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2358 1.34 - 1.46: 1272 1.46 - 1.58: 4459 1.58 - 1.70: 9 1.70 - 1.82: 78 Bond restraints: 8176 Sorted by residual: bond pdb=" C ALA D 154 " pdb=" N TYR D 155 " ideal model delta sigma weight residual 1.334 1.225 0.110 1.27e-02 6.20e+03 7.48e+01 bond pdb=" C TYR D 155 " pdb=" N GLN D 156 " ideal model delta sigma weight residual 1.335 1.435 -0.100 1.30e-02 5.92e+03 5.92e+01 bond pdb=" C LEU B 429 " pdb=" N TYR B 430 " ideal model delta sigma weight residual 1.334 1.263 0.072 1.43e-02 4.89e+03 2.51e+01 bond pdb=" C TYR B 430 " pdb=" N LYS B 431 " ideal model delta sigma weight residual 1.334 1.396 -0.062 1.27e-02 6.20e+03 2.35e+01 bond pdb=" C TYR A 430 " pdb=" N LYS A 431 " ideal model delta sigma weight residual 1.334 1.383 -0.049 1.27e-02 6.20e+03 1.49e+01 ... (remaining 8171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 10803 2.58 - 5.16: 190 5.16 - 7.75: 30 7.75 - 10.33: 1 10.33 - 12.91: 2 Bond angle restraints: 11026 Sorted by residual: angle pdb=" O ALA D 154 " pdb=" C ALA D 154 " pdb=" N TYR D 155 " ideal model delta sigma weight residual 122.07 114.92 7.15 1.03e+00 9.43e-01 4.82e+01 angle pdb=" CA ALA D 154 " pdb=" C ALA D 154 " pdb=" N TYR D 155 " ideal model delta sigma weight residual 117.07 124.02 -6.95 1.14e+00 7.69e-01 3.72e+01 angle pdb=" CA PRO D 168 " pdb=" N PRO D 168 " pdb=" CD PRO D 168 " ideal model delta sigma weight residual 112.00 104.58 7.42 1.40e+00 5.10e-01 2.81e+01 angle pdb=" N TYR A 430 " pdb=" CA TYR A 430 " pdb=" C TYR A 430 " ideal model delta sigma weight residual 111.69 105.72 5.97 1.23e+00 6.61e-01 2.36e+01 angle pdb=" N TYR B 430 " pdb=" CA TYR B 430 " pdb=" C TYR B 430 " ideal model delta sigma weight residual 111.69 105.82 5.87 1.23e+00 6.61e-01 2.28e+01 ... (remaining 11021 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4222 17.94 - 35.88: 641 35.88 - 53.82: 128 53.82 - 71.76: 13 71.76 - 89.70: 8 Dihedral angle restraints: 5012 sinusoidal: 2076 harmonic: 2936 Sorted by residual: dihedral pdb=" CA MET B 512 " pdb=" C MET B 512 " pdb=" N ALA B 513 " pdb=" CA ALA B 513 " ideal model delta harmonic sigma weight residual -180.00 -156.81 -23.19 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA MET A 512 " pdb=" C MET A 512 " pdb=" N ALA A 513 " pdb=" CA ALA A 513 " ideal model delta harmonic sigma weight residual -180.00 -157.55 -22.45 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA LYS C 165 " pdb=" C LYS C 165 " pdb=" N MET C 166 " pdb=" CA MET C 166 " ideal model delta harmonic sigma weight residual -180.00 -160.51 -19.49 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 5009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 896 0.041 - 0.083: 237 0.083 - 0.124: 75 0.124 - 0.165: 16 0.165 - 0.207: 4 Chirality restraints: 1228 Sorted by residual: chirality pdb=" CA PRO C 168 " pdb=" N PRO C 168 " pdb=" C PRO C 168 " pdb=" CB PRO C 168 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA PRO D 168 " pdb=" N PRO D 168 " pdb=" C PRO D 168 " pdb=" CB PRO D 168 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA PRO A 597 " pdb=" N PRO A 597 " pdb=" C PRO A 597 " pdb=" CB PRO A 597 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.95e-01 ... (remaining 1225 not shown) Planarity restraints: 1402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 596 " -0.079 5.00e-02 4.00e+02 1.17e-01 2.20e+01 pdb=" N PRO A 597 " 0.203 5.00e-02 4.00e+02 pdb=" CA PRO A 597 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 597 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 596 " 0.078 5.00e-02 4.00e+02 1.15e-01 2.13e+01 pdb=" N PRO B 597 " -0.200 5.00e-02 4.00e+02 pdb=" CA PRO B 597 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO B 597 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 167 " 0.062 5.00e-02 4.00e+02 8.91e-02 1.27e+01 pdb=" N PRO D 168 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO D 168 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 168 " 0.049 5.00e-02 4.00e+02 ... (remaining 1399 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 181 2.68 - 3.23: 8095 3.23 - 3.79: 12964 3.79 - 4.34: 16329 4.34 - 4.90: 26873 Nonbonded interactions: 64442 Sorted by model distance: nonbonded pdb=" OD1 ASP C 130 " pdb=" OH TYR C 155 " model vdw 2.123 3.040 nonbonded pdb=" NH1 ARG A 467 " pdb=" O LEU A 489 " model vdw 2.159 3.120 nonbonded pdb=" ND2 ASN B 473 " pdb=" OD1 ASP B 486 " model vdw 2.217 3.120 nonbonded pdb=" ND2 ASN A 473 " pdb=" OD1 ASP A 486 " model vdw 2.222 3.120 nonbonded pdb=" N GLU D 8 " pdb=" OE1 GLU D 8 " model vdw 2.276 3.120 ... (remaining 64437 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.320 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 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 0.110 8176 Z= 0.292 Angle : 0.833 12.908 11026 Z= 0.479 Chirality : 0.043 0.207 1228 Planarity : 0.007 0.117 1402 Dihedral : 17.067 89.696 3104 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.68 % Allowed : 25.62 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.27), residues: 968 helix: 1.33 (0.21), residues: 602 sheet: -0.79 (0.86), residues: 40 loop : -1.15 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 58 TYR 0.052 0.003 TYR B 532 PHE 0.014 0.002 PHE B 527 TRP 0.017 0.002 TRP A 368 HIS 0.006 0.001 HIS B 460 Details of bonding type rmsd covalent geometry : bond 0.00533 ( 8176) covalent geometry : angle 0.83300 (11026) hydrogen bonds : bond 0.12080 ( 492) hydrogen bonds : angle 5.26038 ( 1458) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 217 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 GLU cc_start: 0.7258 (mm-30) cc_final: 0.7024 (mm-30) REVERT: C 58 ARG cc_start: 0.7987 (mmt-90) cc_final: 0.7660 (mmm160) REVERT: C 166 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6671 (tmm) REVERT: B 414 LYS cc_start: 0.7581 (mmmm) cc_final: 0.7224 (mtmm) REVERT: B 425 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6729 (mm-30) REVERT: B 512 MET cc_start: 0.6356 (ttp) cc_final: 0.6123 (ptt) REVERT: B 519 MET cc_start: 0.3185 (mmp) cc_final: 0.2708 (mmp) REVERT: D 186 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7962 (mm-30) outliers start: 6 outliers final: 1 residues processed: 221 average time/residue: 0.1028 time to fit residues: 30.5304 Evaluate side-chains 162 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 160 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain C residue 166 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN ** A 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN ** B 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.194166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.159910 restraints weight = 11437.379| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 2.73 r_work: 0.3845 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8176 Z= 0.184 Angle : 0.666 6.442 11026 Z= 0.349 Chirality : 0.042 0.184 1228 Planarity : 0.005 0.066 1402 Dihedral : 4.927 55.466 1089 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.31 % Allowed : 20.98 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.27), residues: 968 helix: 1.61 (0.21), residues: 600 sheet: 0.83 (1.28), residues: 22 loop : -1.31 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 58 TYR 0.032 0.002 TYR D 131 PHE 0.020 0.002 PHE A 599 TRP 0.013 0.002 TRP B 368 HIS 0.003 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 8176) covalent geometry : angle 0.66617 (11026) hydrogen bonds : bond 0.05028 ( 492) hydrogen bonds : angle 4.17330 ( 1458) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 GLN cc_start: 0.6430 (mt0) cc_final: 0.6092 (mm-40) REVERT: A 512 MET cc_start: 0.7068 (ptt) cc_final: 0.6238 (ptm) REVERT: A 581 MET cc_start: 0.7834 (tpt) cc_final: 0.7527 (tpt) REVERT: C 58 ARG cc_start: 0.8245 (mmt-90) cc_final: 0.7859 (mmm160) REVERT: C 155 TYR cc_start: 0.7769 (m-80) cc_final: 0.7197 (m-80) REVERT: C 157 ASP cc_start: 0.8403 (t0) cc_final: 0.8200 (t0) REVERT: B 414 LYS cc_start: 0.7719 (mmmm) cc_final: 0.7497 (mtmm) REVERT: B 541 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7405 (tp) REVERT: B 574 TYR cc_start: 0.5881 (m-10) cc_final: 0.5366 (m-10) REVERT: D 197 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7795 (tt) REVERT: D 200 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7648 (mp10) outliers start: 38 outliers final: 14 residues processed: 209 average time/residue: 0.0744 time to fit residues: 21.9540 Evaluate side-chains 162 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 626 HIS Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 626 HIS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 200 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 38 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 29 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 67 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 48 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN ** A 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 GLN B 386 GLN B 441 GLN ** B 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.202495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.171359 restraints weight = 11301.553| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 2.60 r_work: 0.3982 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8176 Z= 0.134 Angle : 0.612 7.078 11026 Z= 0.318 Chirality : 0.040 0.160 1228 Planarity : 0.004 0.045 1402 Dihedral : 4.448 42.830 1086 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.97 % Allowed : 22.79 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.27), residues: 968 helix: 1.75 (0.21), residues: 596 sheet: 0.10 (0.96), residues: 34 loop : -1.27 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 391 TYR 0.028 0.001 TYR D 131 PHE 0.014 0.001 PHE B 525 TRP 0.011 0.001 TRP A 342 HIS 0.002 0.000 HIS B 477 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 8176) covalent geometry : angle 0.61210 (11026) hydrogen bonds : bond 0.04454 ( 492) hydrogen bonds : angle 4.02942 ( 1458) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 386 GLN cc_start: 0.6510 (mt0) cc_final: 0.6174 (mm-40) REVERT: A 409 MET cc_start: 0.8297 (mtp) cc_final: 0.7875 (mtt) REVERT: A 512 MET cc_start: 0.7309 (ptt) cc_final: 0.6583 (ptm) REVERT: C 58 ARG cc_start: 0.8149 (mmt-90) cc_final: 0.7800 (mmm160) REVERT: C 132 TYR cc_start: 0.8288 (m-80) cc_final: 0.8051 (m-80) REVERT: C 155 TYR cc_start: 0.7781 (m-80) cc_final: 0.7299 (m-80) REVERT: C 157 ASP cc_start: 0.8354 (t0) cc_final: 0.8110 (t0) REVERT: C 200 GLN cc_start: 0.8131 (pt0) cc_final: 0.7509 (pm20) REVERT: B 409 MET cc_start: 0.8269 (mtp) cc_final: 0.7838 (mtt) REVERT: B 512 MET cc_start: 0.6946 (ptt) cc_final: 0.6212 (ptm) REVERT: B 541 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7295 (tp) REVERT: D 58 ARG cc_start: 0.8176 (mmt-90) cc_final: 0.7837 (mmm160) REVERT: D 166 MET cc_start: 0.6923 (OUTLIER) cc_final: 0.6660 (tmm) REVERT: D 197 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7754 (tt) REVERT: D 200 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7431 (mp10) outliers start: 35 outliers final: 16 residues processed: 196 average time/residue: 0.0970 time to fit residues: 25.7684 Evaluate side-chains 173 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 601 GLN Chi-restraints excluded: chain A residue 626 HIS Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain B residue 367 LYS Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 601 GLN Chi-restraints excluded: chain B residue 626 HIS Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 166 MET Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 200 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 63 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 71 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN ** A 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 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 = 0.4394 r_free = 0.4394 target = 0.197954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.164524 restraints weight = 11485.818| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 2.68 r_work: 0.3908 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8176 Z= 0.173 Angle : 0.643 6.966 11026 Z= 0.331 Chirality : 0.042 0.189 1228 Planarity : 0.004 0.046 1402 Dihedral : 4.571 50.244 1086 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.76 % Allowed : 22.90 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.27), residues: 968 helix: 1.67 (0.21), residues: 596 sheet: -0.09 (0.98), residues: 34 loop : -1.25 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 12 TYR 0.033 0.002 TYR D 131 PHE 0.018 0.002 PHE A 599 TRP 0.014 0.002 TRP B 342 HIS 0.004 0.001 HIS B 477 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 8176) covalent geometry : angle 0.64294 (11026) hydrogen bonds : bond 0.04776 ( 492) hydrogen bonds : angle 4.07130 ( 1458) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 386 GLN cc_start: 0.6503 (mt0) cc_final: 0.6140 (mm-40) REVERT: A 409 MET cc_start: 0.8296 (mtp) cc_final: 0.7869 (mtt) REVERT: A 512 MET cc_start: 0.7471 (ptt) cc_final: 0.6725 (ptm) REVERT: C 58 ARG cc_start: 0.8267 (mmt-90) cc_final: 0.7991 (mmp80) REVERT: C 155 TYR cc_start: 0.7786 (m-80) cc_final: 0.7032 (m-80) REVERT: C 157 ASP cc_start: 0.8396 (t0) cc_final: 0.8154 (t0) REVERT: C 200 GLN cc_start: 0.8135 (pt0) cc_final: 0.7628 (pt0) REVERT: B 409 MET cc_start: 0.8302 (mtp) cc_final: 0.7854 (mtt) REVERT: B 478 GLU cc_start: 0.7142 (tm-30) cc_final: 0.6740 (tm-30) REVERT: B 512 MET cc_start: 0.7358 (ptt) cc_final: 0.6640 (ptm) REVERT: B 541 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7590 (tp) REVERT: D 58 ARG cc_start: 0.8280 (mmt-90) cc_final: 0.7993 (mmp80) REVERT: D 170 HIS cc_start: 0.6909 (OUTLIER) cc_final: 0.6501 (t-90) REVERT: D 197 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.7761 (tt) REVERT: D 200 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7424 (mp10) REVERT: D 223 ILE cc_start: 0.7798 (OUTLIER) cc_final: 0.7449 (mp) outliers start: 42 outliers final: 20 residues processed: 196 average time/residue: 0.0843 time to fit residues: 22.5007 Evaluate side-chains 176 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 626 HIS Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain B residue 367 LYS Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 626 HIS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 159 PHE Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 223 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 GLN C 110 HIS ** B 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.195955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.162206 restraints weight = 11450.629| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 2.68 r_work: 0.3880 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8176 Z= 0.197 Angle : 0.675 9.047 11026 Z= 0.345 Chirality : 0.043 0.215 1228 Planarity : 0.004 0.046 1402 Dihedral : 4.845 59.817 1086 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 6.58 % Allowed : 22.56 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.27), residues: 968 helix: 1.53 (0.21), residues: 596 sheet: 0.89 (1.41), residues: 22 loop : -1.33 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 12 TYR 0.035 0.002 TYR D 131 PHE 0.022 0.002 PHE A 599 TRP 0.017 0.002 TRP A 342 HIS 0.004 0.001 HIS A 432 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 8176) covalent geometry : angle 0.67478 (11026) hydrogen bonds : bond 0.05119 ( 492) hydrogen bonds : angle 4.16858 ( 1458) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 165 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 362 THR cc_start: 0.5229 (m) cc_final: 0.5019 (p) REVERT: A 386 GLN cc_start: 0.6570 (mt0) cc_final: 0.6252 (mm-40) REVERT: A 409 MET cc_start: 0.8283 (mtp) cc_final: 0.7706 (mtt) REVERT: A 512 MET cc_start: 0.7549 (ptt) cc_final: 0.6782 (ptm) REVERT: C 155 TYR cc_start: 0.7800 (m-80) cc_final: 0.6817 (m-80) REVERT: C 157 ASP cc_start: 0.8413 (t0) cc_final: 0.8189 (t0) REVERT: C 200 GLN cc_start: 0.8097 (pt0) cc_final: 0.7459 (pm20) REVERT: B 409 MET cc_start: 0.8304 (mtp) cc_final: 0.7725 (mtt) REVERT: B 478 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6772 (tt0) REVERT: B 525 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.7762 (m-10) REVERT: B 541 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7326 (tt) REVERT: B 581 MET cc_start: 0.7826 (mmm) cc_final: 0.7601 (mmm) REVERT: D 170 HIS cc_start: 0.6924 (OUTLIER) cc_final: 0.6471 (t-90) REVERT: D 197 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.7776 (tt) REVERT: D 200 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7432 (mp10) REVERT: D 223 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7498 (mp) outliers start: 58 outliers final: 34 residues processed: 211 average time/residue: 0.0724 time to fit residues: 21.2021 Evaluate side-chains 191 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 601 GLN Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 626 HIS Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain B residue 367 LYS Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 601 GLN Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 626 HIS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 159 PHE Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 223 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 38 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 87 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 GLN ** B 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 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 = 0.4372 r_free = 0.4372 target = 0.195463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.162004 restraints weight = 11370.411| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 2.64 r_work: 0.3885 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 8176 Z= 0.201 Angle : 0.689 10.427 11026 Z= 0.352 Chirality : 0.043 0.204 1228 Planarity : 0.004 0.047 1402 Dihedral : 4.816 52.303 1086 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 6.12 % Allowed : 24.38 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.27), residues: 968 helix: 1.46 (0.21), residues: 596 sheet: 1.04 (1.42), residues: 22 loop : -1.40 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 12 TYR 0.031 0.002 TYR D 131 PHE 0.017 0.002 PHE A 599 TRP 0.016 0.002 TRP A 342 HIS 0.003 0.001 HIS A 432 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 8176) covalent geometry : angle 0.68876 (11026) hydrogen bonds : bond 0.05139 ( 492) hydrogen bonds : angle 4.19838 ( 1458) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 157 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 409 MET cc_start: 0.8295 (mtp) cc_final: 0.7741 (mtt) REVERT: C 104 LEU cc_start: 0.8571 (mt) cc_final: 0.8323 (mt) REVERT: C 155 TYR cc_start: 0.7803 (m-80) cc_final: 0.6809 (m-80) REVERT: C 157 ASP cc_start: 0.8462 (t0) cc_final: 0.8249 (t0) REVERT: C 200 GLN cc_start: 0.8128 (pt0) cc_final: 0.7517 (pm20) REVERT: B 409 MET cc_start: 0.8312 (mtp) cc_final: 0.7747 (mtt) REVERT: B 478 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6722 (tt0) REVERT: B 525 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7564 (m-10) REVERT: D 104 LEU cc_start: 0.8525 (mt) cc_final: 0.8285 (mt) REVERT: D 108 ASP cc_start: 0.7156 (t0) cc_final: 0.6910 (t0) REVERT: D 170 HIS cc_start: 0.6929 (OUTLIER) cc_final: 0.6648 (t-90) REVERT: D 197 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.7773 (tt) REVERT: D 200 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7441 (mp10) REVERT: D 223 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7504 (mp) outliers start: 54 outliers final: 31 residues processed: 200 average time/residue: 0.0756 time to fit residues: 20.8164 Evaluate side-chains 191 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 601 GLN Chi-restraints excluded: chain A residue 626 HIS Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain B residue 367 LYS Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 626 HIS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 159 PHE Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 223 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 76 optimal weight: 7.9990 chunk 72 optimal weight: 0.0370 chunk 16 optimal weight: 0.6980 chunk 87 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.2860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 HIS ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 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 = 0.4414 r_free = 0.4414 target = 0.199020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.165045 restraints weight = 11516.998| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 2.72 r_work: 0.3909 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8176 Z= 0.153 Angle : 0.680 11.976 11026 Z= 0.344 Chirality : 0.041 0.207 1228 Planarity : 0.004 0.046 1402 Dihedral : 4.628 45.444 1086 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 5.33 % Allowed : 25.40 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.27), residues: 968 helix: 1.58 (0.21), residues: 596 sheet: 1.25 (1.44), residues: 22 loop : -1.45 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 12 TYR 0.029 0.001 TYR D 131 PHE 0.013 0.002 PHE B 525 TRP 0.015 0.002 TRP A 342 HIS 0.005 0.001 HIS B 460 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 8176) covalent geometry : angle 0.67973 (11026) hydrogen bonds : bond 0.04719 ( 492) hydrogen bonds : angle 4.11250 ( 1458) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 162 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 409 MET cc_start: 0.8282 (mtp) cc_final: 0.7800 (mtt) REVERT: C 80 ARG cc_start: 0.7351 (mmp80) cc_final: 0.6779 (ptp-110) REVERT: C 104 LEU cc_start: 0.8546 (mt) cc_final: 0.8283 (mt) REVERT: C 155 TYR cc_start: 0.7787 (m-80) cc_final: 0.6839 (m-80) REVERT: C 170 HIS cc_start: 0.6989 (OUTLIER) cc_final: 0.6610 (t-90) REVERT: C 200 GLN cc_start: 0.8160 (pt0) cc_final: 0.7559 (pm20) REVERT: B 409 MET cc_start: 0.8276 (mtp) cc_final: 0.7790 (mtt) REVERT: B 525 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7479 (m-10) REVERT: D 104 LEU cc_start: 0.8481 (mt) cc_final: 0.8233 (mt) REVERT: D 108 ASP cc_start: 0.7274 (t0) cc_final: 0.7058 (t0) REVERT: D 197 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.7726 (tt) REVERT: D 200 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7437 (mp10) outliers start: 47 outliers final: 23 residues processed: 194 average time/residue: 0.0756 time to fit residues: 20.0658 Evaluate side-chains 184 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 626 HIS Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 170 HIS Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 626 HIS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 159 PHE Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 200 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 26 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 68 optimal weight: 20.0000 chunk 65 optimal weight: 0.7980 chunk 69 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.197958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.165415 restraints weight = 11273.435| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 2.60 r_work: 0.3920 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8176 Z= 0.153 Angle : 0.692 11.688 11026 Z= 0.349 Chirality : 0.042 0.181 1228 Planarity : 0.004 0.050 1402 Dihedral : 4.281 20.048 1084 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.65 % Allowed : 25.85 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.27), residues: 968 helix: 1.63 (0.21), residues: 596 sheet: 1.36 (1.45), residues: 22 loop : -1.48 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 12 TYR 0.027 0.001 TYR C 131 PHE 0.011 0.001 PHE B 525 TRP 0.017 0.002 TRP B 342 HIS 0.006 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 8176) covalent geometry : angle 0.69170 (11026) hydrogen bonds : bond 0.04647 ( 492) hydrogen bonds : angle 4.10112 ( 1458) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 409 MET cc_start: 0.8262 (mtp) cc_final: 0.7754 (mtt) REVERT: A 512 MET cc_start: 0.6755 (ptt) cc_final: 0.5841 (ptm) REVERT: C 58 ARG cc_start: 0.8272 (mmt-90) cc_final: 0.8032 (mmt-90) REVERT: C 155 TYR cc_start: 0.7784 (m-80) cc_final: 0.6945 (m-80) REVERT: C 170 HIS cc_start: 0.6881 (OUTLIER) cc_final: 0.6371 (t-90) REVERT: C 200 GLN cc_start: 0.8149 (pt0) cc_final: 0.7546 (pm20) REVERT: B 409 MET cc_start: 0.8297 (mtp) cc_final: 0.7804 (mtt) REVERT: B 478 GLU cc_start: 0.7283 (tm-30) cc_final: 0.6777 (tm-30) REVERT: B 525 PHE cc_start: 0.7868 (OUTLIER) cc_final: 0.7345 (m-10) REVERT: D 58 ARG cc_start: 0.8266 (mmt-90) cc_final: 0.8002 (mmt-90) REVERT: D 104 LEU cc_start: 0.8488 (mt) cc_final: 0.8236 (mt) REVERT: D 111 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6621 (mp) REVERT: D 197 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7741 (tt) REVERT: D 200 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7550 (mp10) REVERT: D 223 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7273 (mp) REVERT: D 224 MET cc_start: 0.7647 (mmm) cc_final: 0.7400 (mmm) outliers start: 41 outliers final: 23 residues processed: 192 average time/residue: 0.0773 time to fit residues: 20.5114 Evaluate side-chains 181 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 626 HIS Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 170 HIS Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 550 HIS Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 626 HIS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 159 PHE Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 223 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 68 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.192045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.158876 restraints weight = 11413.848| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 2.61 r_work: 0.3847 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 8176 Z= 0.258 Angle : 0.810 12.815 11026 Z= 0.410 Chirality : 0.047 0.246 1228 Planarity : 0.005 0.057 1402 Dihedral : 4.624 22.249 1084 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.31 % Allowed : 26.42 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.27), residues: 968 helix: 1.23 (0.21), residues: 594 sheet: 1.23 (1.42), residues: 22 loop : -1.60 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 12 TYR 0.029 0.002 TYR D 131 PHE 0.025 0.002 PHE A 599 TRP 0.017 0.002 TRP B 342 HIS 0.005 0.001 HIS A 432 Details of bonding type rmsd covalent geometry : bond 0.00622 ( 8176) covalent geometry : angle 0.80987 (11026) hydrogen bonds : bond 0.05735 ( 492) hydrogen bonds : angle 4.53965 ( 1458) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 409 MET cc_start: 0.8295 (mtp) cc_final: 0.7734 (mtt) REVERT: A 512 MET cc_start: 0.6972 (ptt) cc_final: 0.5903 (ptm) REVERT: C 155 TYR cc_start: 0.7816 (m-80) cc_final: 0.6851 (m-80) REVERT: C 157 ASP cc_start: 0.8555 (t0) cc_final: 0.8314 (t0) REVERT: C 170 HIS cc_start: 0.6916 (OUTLIER) cc_final: 0.6669 (t-90) REVERT: C 200 GLN cc_start: 0.8185 (pt0) cc_final: 0.7936 (pm20) REVERT: B 409 MET cc_start: 0.8324 (mtp) cc_final: 0.7746 (mtt) REVERT: B 525 PHE cc_start: 0.7850 (OUTLIER) cc_final: 0.7154 (m-10) REVERT: D 155 TYR cc_start: 0.7772 (m-80) cc_final: 0.7330 (m-80) REVERT: D 157 ASP cc_start: 0.8565 (t0) cc_final: 0.8330 (t0) REVERT: D 197 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.7775 (tt) REVERT: D 200 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7422 (mp10) REVERT: D 223 ILE cc_start: 0.7857 (OUTLIER) cc_final: 0.7519 (mp) outliers start: 38 outliers final: 25 residues processed: 181 average time/residue: 0.0728 time to fit residues: 18.4410 Evaluate side-chains 173 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 626 HIS Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 170 HIS Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 550 HIS Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 626 HIS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 159 PHE Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 223 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 16 optimal weight: 0.0570 chunk 85 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.197547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.165193 restraints weight = 11504.224| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 2.61 r_work: 0.3914 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8176 Z= 0.158 Angle : 0.748 14.247 11026 Z= 0.374 Chirality : 0.044 0.231 1228 Planarity : 0.004 0.055 1402 Dihedral : 4.461 20.894 1084 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.29 % Allowed : 27.21 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.27), residues: 968 helix: 1.45 (0.21), residues: 594 sheet: 1.48 (1.43), residues: 22 loop : -1.54 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 12 TYR 0.027 0.001 TYR D 131 PHE 0.010 0.001 PHE A 599 TRP 0.020 0.002 TRP B 342 HIS 0.011 0.001 HIS B 460 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 8176) covalent geometry : angle 0.74764 (11026) hydrogen bonds : bond 0.04874 ( 492) hydrogen bonds : angle 4.36160 ( 1458) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 MET cc_start: 0.7807 (tmm) cc_final: 0.7603 (tmm) REVERT: A 386 GLN cc_start: 0.6553 (mt0) cc_final: 0.6228 (mm-40) REVERT: A 409 MET cc_start: 0.8252 (mtp) cc_final: 0.7758 (mtt) REVERT: A 512 MET cc_start: 0.6772 (ptt) cc_final: 0.5854 (ptm) REVERT: C 155 TYR cc_start: 0.7776 (m-80) cc_final: 0.6810 (m-80) REVERT: C 200 GLN cc_start: 0.8157 (pt0) cc_final: 0.7513 (pm20) REVERT: C 224 MET cc_start: 0.7720 (mmm) cc_final: 0.7465 (mmm) REVERT: B 409 MET cc_start: 0.8283 (mtp) cc_final: 0.7789 (mtt) REVERT: B 525 PHE cc_start: 0.7730 (OUTLIER) cc_final: 0.7017 (m-10) REVERT: B 541 LEU cc_start: 0.7120 (tp) cc_final: 0.6904 (tp) REVERT: D 197 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7743 (tt) REVERT: D 200 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7533 (mp10) REVERT: D 223 ILE cc_start: 0.7674 (OUTLIER) cc_final: 0.7360 (mp) outliers start: 29 outliers final: 22 residues processed: 181 average time/residue: 0.0753 time to fit residues: 19.4982 Evaluate side-chains 178 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 626 HIS Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 550 HIS Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 626 HIS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 159 PHE Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 223 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 89 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 71 optimal weight: 0.3980 chunk 8 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 20 optimal weight: 20.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.199298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.166960 restraints weight = 11380.962| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 2.58 r_work: 0.3931 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8176 Z= 0.145 Angle : 0.732 14.138 11026 Z= 0.364 Chirality : 0.043 0.218 1228 Planarity : 0.004 0.057 1402 Dihedral : 4.351 19.707 1084 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.06 % Allowed : 27.32 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.27), residues: 968 helix: 1.46 (0.21), residues: 606 sheet: 0.28 (1.03), residues: 34 loop : -1.36 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 12 TYR 0.024 0.001 TYR D 131 PHE 0.008 0.001 PHE B 525 TRP 0.017 0.002 TRP B 342 HIS 0.010 0.001 HIS B 460 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 8176) covalent geometry : angle 0.73175 (11026) hydrogen bonds : bond 0.04564 ( 492) hydrogen bonds : angle 4.27520 ( 1458) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1675.03 seconds wall clock time: 29 minutes 35.79 seconds (1775.79 seconds total)