Starting phenix.real_space_refine on Wed Feb 12 12:20:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cpd_16779/02_2025/8cpd_16779.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cpd_16779/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8cpd_16779/02_2025/8cpd_16779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cpd_16779/02_2025/8cpd_16779.map" model { file = "/net/cci-nas-00/data/ceres_data/8cpd_16779/02_2025/8cpd_16779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cpd_16779/02_2025/8cpd_16779.cif" } resolution = 3.46 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= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.32, per 1000 atoms: 0.66 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: 1.93 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.64 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: 2.12 Time building geometry restraints manager: 2.26 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: 0.02 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: 0.960 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.820 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.520 ------------------------------------------------------------------------------- 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= 0.339 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (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 TRP 0.017 0.002 TRP A 368 HIS 0.006 0.001 HIS B 460 PHE 0.014 0.002 PHE B 527 TYR 0.052 0.003 TYR B 532 ARG 0.010 0.001 ARG D 58 *********************** 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 : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 GLU cc_start: 0.7258 (mm-30) cc_final: 0.7040 (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: 0.6672 (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: 0.6731 (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: 0.2705 (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: 0.2169 time to fit residues: 63.5759 Evaluate side-chains 160 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 158 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 81 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 29 optimal weight: 0.0030 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.199670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.166201 restraints weight = 11283.128| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 2.71 r_work: 0.3912 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8176 Z= 0.195 Angle : 0.623 5.975 11026 Z= 0.327 Chirality : 0.040 0.150 1228 Planarity : 0.005 0.064 1402 Dihedral : 4.771 55.632 1089 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.29 % Allowed : 21.20 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.27), residues: 968 helix: 1.80 (0.21), residues: 600 sheet: -0.37 (1.09), residues: 22 loop : -1.22 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 368 HIS 0.002 0.001 HIS A 477 PHE 0.015 0.002 PHE B 525 TYR 0.032 0.002 TYR D 131 ARG 0.008 0.001 ARG B 391 *********************** 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 209 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 GLN cc_start: 0.6355 (mt0) cc_final: 0.6027 (mm-40) REVERT: A 512 MET cc_start: 0.6914 (ptt) cc_final: 0.6117 (ptm) REVERT: C 58 ARG cc_start: 0.8167 (mmt-90) cc_final: 0.7913 (mmp80) REVERT: B 414 LYS cc_start: 0.7707 (mmmm) cc_final: 0.7353 (mtmm) REVERT: B 574 TYR cc_start: 0.5733 (m-10) cc_final: 0.5282 (m-10) REVERT: D 58 ARG cc_start: 0.8205 (mmt-90) cc_final: 0.7856 (mmm160) REVERT: D 197 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7770 (tt) REVERT: D 200 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7570 (mp10) outliers start: 29 outliers final: 10 residues processed: 200 average time/residue: 0.2011 time to fit residues: 55.5047 Evaluate side-chains 158 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 15 LEU 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 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 70 optimal weight: 0.9990 chunk 36 optimal weight: 0.0370 chunk 53 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 92 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.3664 ------------------------------------------------------------------------------- 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** B 436 GLN B 441 GLN ** B 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.200979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.167768 restraints weight = 11447.578| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 2.70 r_work: 0.3932 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8176 Z= 0.225 Angle : 0.626 8.390 11026 Z= 0.327 Chirality : 0.041 0.168 1228 Planarity : 0.004 0.045 1402 Dihedral : 4.262 30.476 1086 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.97 % Allowed : 23.36 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.27), residues: 968 helix: 1.68 (0.21), residues: 606 sheet: -0.24 (1.16), residues: 22 loop : -1.24 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 342 HIS 0.002 0.001 HIS A 477 PHE 0.015 0.002 PHE A 599 TYR 0.033 0.002 TYR D 131 ARG 0.010 0.001 ARG B 391 *********************** 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 204 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 GLN cc_start: 0.6421 (mt0) cc_final: 0.6085 (mm-40) REVERT: A 409 MET cc_start: 0.8281 (mtp) cc_final: 0.7815 (mtt) REVERT: A 512 MET cc_start: 0.7341 (ptt) cc_final: 0.6553 (ptm) REVERT: C 58 ARG cc_start: 0.8183 (mmt-90) cc_final: 0.7811 (mmm160) REVERT: C 197 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.7714 (tt) REVERT: C 200 GLN cc_start: 0.8121 (pt0) cc_final: 0.7540 (pm20) REVERT: B 409 MET cc_start: 0.8286 (mtp) cc_final: 0.7802 (mtt) REVERT: B 512 MET cc_start: 0.7236 (ptt) cc_final: 0.6352 (ptm) REVERT: D 58 ARG cc_start: 0.8202 (mmt-90) cc_final: 0.7963 (mmp80) REVERT: D 166 MET cc_start: 0.6934 (OUTLIER) cc_final: 0.6658 (tmm) REVERT: D 197 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7751 (tt) REVERT: D 200 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7431 (mp10) outliers start: 35 outliers final: 18 residues processed: 195 average time/residue: 0.2285 time to fit residues: 59.8865 Evaluate side-chains 173 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 LYS 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 626 HIS Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain B residue 367 LYS Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 540 GLU 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 9 LEU Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 143 THR 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 35 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 36 optimal weight: 0.0870 chunk 29 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- 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 ** 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 = 0.4320 r_free = 0.4320 target = 0.190714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.155764 restraints weight = 11567.475| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 2.74 r_work: 0.3802 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 8176 Z= 0.325 Angle : 0.692 8.040 11026 Z= 0.358 Chirality : 0.043 0.196 1228 Planarity : 0.004 0.047 1402 Dihedral : 4.456 34.695 1086 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 5.22 % Allowed : 22.22 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.27), residues: 968 helix: 1.47 (0.21), residues: 600 sheet: 0.76 (1.36), residues: 22 loop : -1.43 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 342 HIS 0.003 0.001 HIS A 432 PHE 0.022 0.002 PHE A 599 TYR 0.033 0.002 TYR D 131 ARG 0.005 0.001 ARG C 12 *********************** 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 205 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 159 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 GLN cc_start: 0.6329 (mt0) cc_final: 0.6090 (mm-40) REVERT: A 409 MET cc_start: 0.8249 (mtp) cc_final: 0.7804 (mtt) REVERT: A 512 MET cc_start: 0.7529 (ptt) cc_final: 0.6718 (ptm) REVERT: A 542 MET cc_start: 0.6164 (tpp) cc_final: 0.5946 (tpp) REVERT: C 197 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8136 (tt) REVERT: C 200 GLN cc_start: 0.8159 (pt0) cc_final: 0.7870 (pt0) REVERT: B 409 MET cc_start: 0.8271 (mtp) cc_final: 0.7814 (mtt) REVERT: B 512 MET cc_start: 0.7419 (ptt) cc_final: 0.6638 (ptm) REVERT: D 155 TYR cc_start: 0.7691 (m-80) cc_final: 0.7468 (m-80) REVERT: D 170 HIS cc_start: 0.7049 (OUTLIER) cc_final: 0.6625 (t-90) REVERT: D 197 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.7767 (tt) REVERT: D 200 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7489 (mp10) REVERT: D 223 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7520 (mp) outliers start: 46 outliers final: 22 residues processed: 197 average time/residue: 0.2017 time to fit residues: 53.7691 Evaluate side-chains 175 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 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 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 C residue 197 LEU Chi-restraints excluded: chain B residue 367 LYS Chi-restraints excluded: chain B residue 400 THR 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 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 16 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 71 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.195522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.160619 restraints weight = 11308.715| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 2.78 r_work: 0.3859 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8176 Z= 0.187 Angle : 0.622 9.515 11026 Z= 0.320 Chirality : 0.040 0.160 1228 Planarity : 0.004 0.046 1402 Dihedral : 4.402 39.289 1086 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.42 % Allowed : 23.02 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.27), residues: 968 helix: 1.67 (0.21), residues: 598 sheet: 1.10 (1.44), residues: 22 loop : -1.40 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 342 HIS 0.002 0.000 HIS A 477 PHE 0.021 0.001 PHE B 525 TYR 0.033 0.001 TYR C 131 ARG 0.006 0.000 ARG C 12 *********************** 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 200 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 GLN cc_start: 0.6352 (mt0) cc_final: 0.6068 (mm-40) REVERT: A 409 MET cc_start: 0.8212 (mtp) cc_final: 0.7717 (mtt) REVERT: C 58 ARG cc_start: 0.8262 (mmt-90) cc_final: 0.7843 (mmm160) REVERT: C 200 GLN cc_start: 0.8152 (pt0) cc_final: 0.7526 (pm20) REVERT: B 367 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8195 (tttp) REVERT: B 409 MET cc_start: 0.8227 (mtp) cc_final: 0.7718 (mtt) REVERT: B 581 MET cc_start: 0.7708 (mmm) cc_final: 0.7438 (mmm) REVERT: D 58 ARG cc_start: 0.8276 (mmt-90) cc_final: 0.7856 (mmm160) REVERT: D 108 ASP cc_start: 0.7443 (t0) cc_final: 0.7223 (t0) REVERT: D 170 HIS cc_start: 0.6979 (OUTLIER) cc_final: 0.6568 (t-90) REVERT: D 197 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7712 (tt) REVERT: D 200 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7480 (mp10) REVERT: D 223 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7412 (mp) outliers start: 39 outliers final: 19 residues processed: 191 average time/residue: 0.2019 time to fit residues: 52.7316 Evaluate side-chains 174 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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 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 43 GLU 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 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 9 LEU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 71 LYS 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 11 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 16 optimal weight: 0.0770 chunk 21 optimal weight: 0.9980 overall best weight: 1.1540 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.194541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.160256 restraints weight = 11406.404| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 2.70 r_work: 0.3851 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8176 Z= 0.207 Angle : 0.637 9.577 11026 Z= 0.327 Chirality : 0.041 0.165 1228 Planarity : 0.004 0.047 1402 Dihedral : 4.387 43.340 1086 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.31 % Allowed : 24.60 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.27), residues: 968 helix: 1.66 (0.21), residues: 600 sheet: 0.15 (1.04), residues: 34 loop : -1.27 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 342 HIS 0.003 0.001 HIS B 460 PHE 0.015 0.001 PHE B 525 TYR 0.032 0.002 TYR C 131 ARG 0.011 0.001 ARG C 12 *********************** 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 193 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 367 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8144 (tttp) REVERT: A 386 GLN cc_start: 0.6372 (mt0) cc_final: 0.6082 (mm-40) REVERT: A 409 MET cc_start: 0.8199 (mtp) cc_final: 0.7647 (mtt) REVERT: C 58 ARG cc_start: 0.8273 (mmt-90) cc_final: 0.7850 (mmm160) REVERT: C 157 ASP cc_start: 0.8439 (t0) cc_final: 0.8225 (t0) REVERT: C 170 HIS cc_start: 0.6768 (OUTLIER) cc_final: 0.6428 (t-90) REVERT: C 197 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.7704 (tt) REVERT: C 200 GLN cc_start: 0.8158 (pt0) cc_final: 0.7532 (pm20) REVERT: B 367 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8214 (tttp) REVERT: B 409 MET cc_start: 0.8231 (mtp) cc_final: 0.7707 (mtt) REVERT: B 525 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.7357 (m-10) REVERT: D 58 ARG cc_start: 0.8302 (mmt-90) cc_final: 0.8044 (mmt-90) REVERT: D 108 ASP cc_start: 0.7417 (t0) cc_final: 0.7182 (t0) REVERT: D 170 HIS cc_start: 0.6934 (OUTLIER) cc_final: 0.6517 (t-90) REVERT: D 197 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7728 (tt) REVERT: D 200 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7564 (mp10) REVERT: D 223 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7410 (mp) outliers start: 38 outliers final: 18 residues processed: 183 average time/residue: 0.2012 time to fit residues: 49.9799 Evaluate side-chains 176 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 567 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 170 HIS Chi-restraints excluded: chain C residue 197 LEU 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 525 PHE 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 9 LEU Chi-restraints excluded: chain D residue 15 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 20 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 84 optimal weight: 0.0370 chunk 30 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 69 optimal weight: 0.0170 chunk 24 optimal weight: 0.7980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.196861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.162746 restraints weight = 11395.593| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 2.71 r_work: 0.3884 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8176 Z= 0.175 Angle : 0.633 11.985 11026 Z= 0.321 Chirality : 0.040 0.165 1228 Planarity : 0.004 0.047 1402 Dihedral : 4.330 47.200 1086 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.51 % Allowed : 25.06 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.27), residues: 968 helix: 1.78 (0.21), residues: 598 sheet: 0.15 (1.03), residues: 34 loop : -1.20 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 342 HIS 0.005 0.001 HIS B 460 PHE 0.011 0.001 PHE B 525 TYR 0.028 0.001 TYR C 131 ARG 0.011 0.000 ARG C 12 *********************** 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 188 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 367 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8166 (tttp) REVERT: A 386 GLN cc_start: 0.6375 (mt0) cc_final: 0.6068 (mm-40) REVERT: A 409 MET cc_start: 0.8175 (mtp) cc_final: 0.7686 (mtt) REVERT: C 58 ARG cc_start: 0.8250 (mmt-90) cc_final: 0.8024 (mmt-90) REVERT: C 157 ASP cc_start: 0.8396 (t0) cc_final: 0.8171 (t0) REVERT: C 170 HIS cc_start: 0.6629 (OUTLIER) cc_final: 0.6283 (t-90) REVERT: C 197 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.7661 (tt) REVERT: C 200 GLN cc_start: 0.8154 (pt0) cc_final: 0.7548 (pm20) REVERT: C 224 MET cc_start: 0.7597 (mmm) cc_final: 0.7381 (mmm) REVERT: B 409 MET cc_start: 0.8241 (mtp) cc_final: 0.7728 (mtt) REVERT: B 525 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.7234 (m-10) REVERT: D 58 ARG cc_start: 0.8255 (mmt-90) cc_final: 0.7812 (mmm160) REVERT: D 108 ASP cc_start: 0.7390 (t0) cc_final: 0.7171 (t0) REVERT: D 166 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7011 (ttp) REVERT: D 170 HIS cc_start: 0.6894 (OUTLIER) cc_final: 0.6467 (t-90) REVERT: D 197 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7714 (tt) REVERT: D 200 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7575 (mp10) outliers start: 31 outliers final: 16 residues processed: 178 average time/residue: 0.2092 time to fit residues: 50.2183 Evaluate side-chains 170 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 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 111 LEU Chi-restraints excluded: chain C residue 170 HIS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain B residue 396 VAL 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 601 GLN Chi-restraints excluded: chain B residue 626 HIS Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 166 MET Chi-restraints excluded: chain D residue 170 HIS 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 60 optimal weight: 6.9990 chunk 51 optimal weight: 0.0770 chunk 5 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 71 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.9944 ------------------------------------------------------------------------------- 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 ** 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 = 0.4337 r_free = 0.4337 target = 0.192020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.157313 restraints weight = 11488.333| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 2.70 r_work: 0.3819 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8176 Z= 0.273 Angle : 0.703 11.828 11026 Z= 0.356 Chirality : 0.043 0.224 1228 Planarity : 0.004 0.051 1402 Dihedral : 4.505 53.431 1086 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.42 % Allowed : 25.06 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.27), residues: 968 helix: 1.59 (0.21), residues: 596 sheet: 0.06 (1.04), residues: 34 loop : -1.16 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 342 HIS 0.003 0.001 HIS A 432 PHE 0.019 0.002 PHE B 599 TYR 0.031 0.002 TYR C 131 ARG 0.012 0.001 ARG C 12 *********************** 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 195 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 409 MET cc_start: 0.8215 (mtp) cc_final: 0.7699 (mtt) REVERT: C 58 ARG cc_start: 0.8334 (mmt-90) cc_final: 0.8091 (mmt-90) REVERT: C 157 ASP cc_start: 0.8401 (t0) cc_final: 0.8172 (t0) REVERT: C 170 HIS cc_start: 0.6762 (OUTLIER) cc_final: 0.6337 (t-90) REVERT: C 197 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.7689 (tt) REVERT: C 200 GLN cc_start: 0.8169 (pt0) cc_final: 0.7582 (pm20) REVERT: B 409 MET cc_start: 0.8254 (mtp) cc_final: 0.7686 (mtt) REVERT: B 525 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.7213 (m-10) REVERT: D 58 ARG cc_start: 0.8344 (mmt-90) cc_final: 0.8095 (mmt-90) REVERT: D 170 HIS cc_start: 0.6983 (OUTLIER) cc_final: 0.6553 (t-90) REVERT: D 197 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7749 (tt) REVERT: D 200 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7574 (mp10) REVERT: D 223 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7408 (mp) outliers start: 39 outliers final: 23 residues processed: 187 average time/residue: 0.2049 time to fit residues: 52.0920 Evaluate side-chains 174 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 550 HIS 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 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 111 LEU Chi-restraints excluded: chain C residue 170 HIS Chi-restraints excluded: chain C residue 197 LEU 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 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 9 LEU Chi-restraints excluded: chain D residue 15 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 24 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 20.0000 chunk 65 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 67 optimal weight: 7.9990 chunk 64 optimal weight: 0.0470 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.7080 ------------------------------------------------------------------------------- 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 ** 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 = 0.4379 r_free = 0.4379 target = 0.196056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.161652 restraints weight = 11577.870| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 2.72 r_work: 0.3868 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8176 Z= 0.194 Angle : 0.705 13.703 11026 Z= 0.352 Chirality : 0.042 0.239 1228 Planarity : 0.004 0.048 1402 Dihedral : 4.564 59.017 1086 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.40 % Allowed : 26.19 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.27), residues: 968 helix: 1.73 (0.21), residues: 594 sheet: 0.15 (1.01), residues: 34 loop : -1.07 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 342 HIS 0.007 0.001 HIS B 460 PHE 0.008 0.001 PHE B 527 TYR 0.027 0.001 TYR C 131 ARG 0.013 0.001 ARG C 12 *********************** 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 183 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 GLN cc_start: 0.6368 (mt0) cc_final: 0.6074 (mm-40) REVERT: A 409 MET cc_start: 0.8185 (mtp) cc_final: 0.7691 (mtt) REVERT: C 58 ARG cc_start: 0.8264 (mmt-90) cc_final: 0.7814 (mmm160) REVERT: C 170 HIS cc_start: 0.6674 (OUTLIER) cc_final: 0.6225 (t-90) REVERT: C 197 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.7711 (tt) REVERT: C 200 GLN cc_start: 0.8213 (pt0) cc_final: 0.7624 (pm20) REVERT: B 409 MET cc_start: 0.8234 (mtp) cc_final: 0.7721 (mtt) REVERT: B 525 PHE cc_start: 0.7620 (OUTLIER) cc_final: 0.6860 (m-10) REVERT: D 58 ARG cc_start: 0.8265 (mmt-90) cc_final: 0.7863 (mmm160) REVERT: D 197 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7712 (tt) REVERT: D 200 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7583 (mp10) outliers start: 30 outliers final: 20 residues processed: 175 average time/residue: 0.2010 time to fit residues: 47.5328 Evaluate side-chains 172 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 541 LEU Chi-restraints excluded: chain A residue 550 HIS 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 626 HIS Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 170 HIS Chi-restraints excluded: chain C residue 197 LEU 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 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 9 LEU Chi-restraints excluded: chain D residue 15 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 70 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 63 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 ** 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 = 0.4325 r_free = 0.4325 target = 0.190758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.156240 restraints weight = 11415.963| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 2.66 r_work: 0.3802 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8176 Z= 0.303 Angle : 0.788 14.339 11026 Z= 0.389 Chirality : 0.045 0.266 1228 Planarity : 0.004 0.053 1402 Dihedral : 4.671 54.467 1086 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.06 % Allowed : 27.10 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.27), residues: 968 helix: 1.47 (0.21), residues: 598 sheet: 0.08 (1.02), residues: 34 loop : -1.09 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 342 HIS 0.004 0.001 HIS B 460 PHE 0.016 0.002 PHE B 599 TYR 0.030 0.002 TYR C 131 ARG 0.013 0.001 ARG C 12 ********************** 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 176 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 GLN cc_start: 0.6457 (mt0) cc_final: 0.6119 (mm-40) REVERT: A 409 MET cc_start: 0.8215 (mtp) cc_final: 0.7715 (mtt) REVERT: C 58 ARG cc_start: 0.8345 (mmt-90) cc_final: 0.8101 (mmt-90) REVERT: C 197 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.7710 (tt) REVERT: C 200 GLN cc_start: 0.8229 (pt0) cc_final: 0.7676 (pm20) REVERT: B 409 MET cc_start: 0.8260 (mtp) cc_final: 0.7693 (mtt) REVERT: B 525 PHE cc_start: 0.7572 (OUTLIER) cc_final: 0.7035 (m-10) REVERT: D 58 ARG cc_start: 0.8386 (mmt-90) cc_final: 0.8145 (mmt-90) REVERT: D 197 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7722 (tt) REVERT: D 200 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7590 (mp10) outliers start: 27 outliers final: 20 residues processed: 172 average time/residue: 0.2007 time to fit residues: 47.2517 Evaluate side-chains 165 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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 519 MET Chi-restraints excluded: chain A residue 550 HIS 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 626 HIS Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 197 LEU 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 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 9 LEU Chi-restraints excluded: chain D residue 15 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 76 optimal weight: 8.9990 chunk 27 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 84 optimal weight: 9.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- 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 ** 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 = 0.4310 r_free = 0.4310 target = 0.189369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.155011 restraints weight = 11483.740| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.65 r_work: 0.3792 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8176 Z= 0.317 Angle : 0.797 16.084 11026 Z= 0.396 Chirality : 0.045 0.256 1228 Planarity : 0.005 0.053 1402 Dihedral : 4.460 19.962 1084 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.74 % Allowed : 26.19 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.27), residues: 968 helix: 1.33 (0.21), residues: 592 sheet: 0.05 (1.04), residues: 34 loop : -1.17 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 342 HIS 0.006 0.001 HIS B 460 PHE 0.018 0.002 PHE B 599 TYR 0.030 0.002 TYR C 131 ARG 0.013 0.001 ARG C 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3444.96 seconds wall clock time: 62 minutes 11.37 seconds (3731.37 seconds total)